ClinVar Genomic variation as it relates to human health
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3
Variation ID: 155309 Accession: VCV000155309.2
- Type and length
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copy number gain, 33,043,324 bp
- Location
-
Cytogenetic: 21q11.2-22.3 21: 7749532-46677460 (GRCh38) [ NCBI UCSC ] 21: 15006458-48097372 (GRCh37) [ NCBI UCSC ] 21: 13928329-46921800 (NCBI36) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jul 13, 2015 Jul 13, 2015 Feb 11, 2016 - HGVS
-
Nucleotide Protein Molecular
consequenceNC_000021.9:g.(?_7749532)_(46677460_?)dup NC_000021.8:g.(?_15006458)_(48097372_?)dup - Protein change
- -
- Other names
- -
- Canonical SPDI
- -
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
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dbVar: nssv13652346 dbVar: nssv13652629 dbVar: nssv13654209 dbVar: nssv13654394 dbVar: nssv13654396 dbVar: nssv13655015 dbVar: nssv13656300 dbVar: nssv13656499 dbVar: nssv13656550 dbVar: nssv14081940 dbVar: nssv14081978 dbVar: nssv14082011 dbVar: nssv14082063 dbVar: nssv14082192 dbVar: nssv14082235 dbVar: nssv14082253 dbVar: nssv14082328 dbVar: nssv14082459 dbVar: nssv14082517 dbVar: nssv3395236 dbVar: nssv3395237 dbVar: nssv3395239 dbVar: nssv3395241 dbVar: nssv3395242 dbVar: nssv3395397 dbVar: nssv3395405 dbVar: nssv3395406 dbVar: nssv3396756 dbVar: nssv3396829 dbVar: nssv3396837 dbVar: nssv3396841 dbVar: nsv995205 dbVar: nssv13638566 dbVar: nssv13638887 dbVar: nssv13638889 dbVar: nssv13638899 dbVar: nssv13638962 dbVar: nssv13639270 dbVar: nssv13639279 dbVar: nssv13639646 dbVar: nssv13639833 dbVar: nssv13639996 dbVar: nssv13640074 dbVar: nssv13640441 dbVar: nssv13640447 dbVar: nssv13640758 dbVar: nssv13640770 dbVar: nssv13640904 dbVar: nssv13641141 dbVar: nssv13641419 dbVar: nssv13641500 dbVar: nssv13641767 dbVar: nssv13641982 dbVar: nssv13642432 dbVar: nssv13642635 dbVar: nssv13642721 dbVar: nssv13645299 dbVar: nssv13646001 dbVar: nssv13646288 dbVar: nssv13646666 dbVar: nssv13648155 dbVar: nssv13648392 dbVar: nssv13649695 dbVar: nssv13649771 dbVar: nssv13650008 dbVar: nssv13650396 dbVar: nssv13650881 dbVar: nssv13651340 dbVar: nssv13643888 dbVar: nssv13643964 dbVar: nssv13643971 dbVar: nssv13642967 dbVar: nssv13642999 dbVar: nssv13643605 dbVar: nssv13643836 VarSome
Genes
There are 1152 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37 , NCBI36) and ClinGen Dosage Sensitivity Map.
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
|
See cases
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Pathogenic (1) |
no assertion criteria provided
|
Feb 11, 2016 | RCV000143376.6 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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|---|---|---|---|---|---|
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Pathogenic
(Feb 11, 2016)
|
no assertion criteria provided
Method: clinical testing
|
See cases
Affected status: yes
Allele origin:
unknown
|
ISCA site 1
Additional submitter:
International Standards For Cytogenomic Arrays Consortium (ISCA)
Accession: SCV000182621.4
First in ClinVar: Sep 01, 2014 Last updated: Jul 13, 2015
Comments (2):
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For … (more)
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011|/pubmed/21844811], please see [nstd101|/dbvar/studies/nstd101/]. (less)
|
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Muscular hypotonia (present) , Ventricular septal defect (present) , Bilateral single transverse palmar creases (present)
Method: Microarray
Result:
Pass
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 3:
Number of individuals with the variant: 1
Clinical Features:
Epicanthus (present) , Low-set ears (present) , Bilateral single transverse palmar creases (present)
Method: Microarray
Result:
Pass
Observation 4:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 5:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 6:
Number of individuals with the variant: 1
Clinical Features:
Retinal detachment (present) , Delayed speech and language development (present) , Intellectual disability (present) , Seizures (present) , Spasticity (present) , Tetralogy of Fallot (present) … (more)
Retinal detachment (present) , Delayed speech and language development (present) , Intellectual disability (present) , Seizures (present) , Spasticity (present) , Tetralogy of Fallot (present) , Gastroesophageal reflux (present) , Intracranial hemorrhage (present) , Delayed gross motor development (present) , Short stature (present) , Acute lymphoblastic leukemia (present) , Delayed fine motor development (present) (less)
Age: 10-19 years
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 7:
Number of individuals with the variant: 1
Clinical Features:
Low-set ears (present) , Wide nasal bridge (present) , Upslanted palpebral fissure (present) , Abnormal facial shape (present) , Protruding tongue (present)
Method: Microarray
Result:
Pass
Observation 8:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 9:
Number of individuals with the variant: 1
Clinical Features:
Premature birth (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 10:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Sex: female
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 11:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 12:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 13:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 14:
Number of individuals with the variant: 1
Clinical Features:
Macroglossia (present) , Sandal gap (present) , Abnormal facial shape (present) , Thoracic hypoplasia (present) , Redundant neck skin (present) , Bilateral single transverse palmar … (more)
Macroglossia (present) , Sandal gap (present) , Abnormal facial shape (present) , Thoracic hypoplasia (present) , Redundant neck skin (present) , Bilateral single transverse palmar creases (present) (less)
Method: Microarray
Result:
Pass
Observation 15:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 16:
Number of individuals with the variant: 1
Clinical Features:
Muscular hypotonia (present) , Sandal gap (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 17:
Number of individuals with the variant: 1
Clinical Features:
Stereotypy (present) , Short stature (present) , Micromelia (present)
Age: 0-9 years
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 18:
Number of individuals with the variant: 1
Clinical Features:
Hypertelorism (present) , Abnormal facial shape (present) , Bilateral single transverse palmar creases (present)
Method: Microarray
Result:
Pass
Observation 19:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 20:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 21:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 22:
Number of individuals with the variant: 1
Clinical Features:
Wide nasal bridge (present) , Overfolding of the superior helices (present) , Protruding tongue (present)
Method: Microarray
Result:
Pass
Observation 23:
Number of individuals with the variant: 1
Clinical Features:
Hydronephrosis (present) , Muscular hypotonia (present) , Abnormality of the amniotic fluid (present) , Premature birth (present) , Potter facies (present) , Pulmonary hypoplasia (present) … (more)
Hydronephrosis (present) , Muscular hypotonia (present) , Abnormality of the amniotic fluid (present) , Premature birth (present) , Potter facies (present) , Pulmonary hypoplasia (present) , Abnormal facial shape (present) (less)
Method: Microarray
Result:
Pass
Observation 24:
Number of individuals with the variant: 1
Clinical Features:
obsolete Malformation of the heart and great vessels (present)
Method: Microarray
Result:
Pass
Observation 25:
Number of individuals with the variant: 1
Clinical Features:
Respiratory distress (present)
Sex: female
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 26:
Number of individuals with the variant: 1
Clinical Features:
Polyphagia (present)
Method: Microarray
Result:
Pass
Observation 27:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 28:
Number of individuals with the variant: 1
Clinical Features:
Thickened nuchal skin fold (present) , Muscular hypotonia (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 29:
Number of individuals with the variant: 1
Clinical Features:
Muscular hypotonia (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 30:
Number of individuals with the variant: 1
Clinical Features:
Thickened nuchal skin fold (present) , Deep plantar creases (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 31:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 32:
Number of individuals with the variant: 1
Clinical Features:
Ventricular septal defect (present)
Method: Microarray
Result:
Pass
Observation 33:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 34:
Number of individuals with the variant: 1
Clinical Features:
Ventricular septal defect (present) , Atrial septal defect (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 35:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present) , Short stature (present)
Method: Microarray
Result:
Pass
Observation 36:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 37:
Number of individuals with the variant: 1
Clinical Features:
Abnormal heart morphology (present) , Patent ductus arteriosus (present)
Method: Microarray
Result:
Pass
Observation 38:
Number of individuals with the variant: 1
Clinical Features:
Epicanthus (present) , Muscular hypotonia (present) , Ventricular septal defect (present) , Aplasia/Hypoplasia of the middle phalanx of the 5th finger (present)
Method: Microarray
Result:
Pass
Observation 39:
Number of individuals with the variant: 1
Clinical Features:
Cleft palate (present) , Cleft upper lip (present)
Method: Microarray
Result:
Pass
Observation 40:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 41:
Number of individuals with the variant: 1
Clinical Features:
Syndactyly (present) , Muscular hypotonia (present) , Umbilical hernia (present) , Abnormal facial shape (present)
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 42:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 43:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 44:
Number of individuals with the variant: 1
Clinical Features:
Atrial septal defect (present) , Patent ductus arteriosus (present)
Method: Microarray
Result:
Pass
Observation 45:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 46:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 47:
Number of individuals with the variant: 1
Clinical Features:
Failure to thrive (present)
Method: Microarray
Result:
Pass
Observation 48:
Number of individuals with the variant: 1
Clinical Features:
Premature birth (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 49:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 50:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 51:
Number of individuals with the variant: 1
Clinical Features:
Microcephaly (present)
Method: Microarray
Result:
Pass
Observation 52:
Number of individuals with the variant: 1
Clinical Features:
Abnormality of the face (present) , Abnormality of the ear (present) , Syndactyly (present) , Premature birth (present) , Talipes equinovarus (present) , Tongue thrusting … (more)
Abnormality of the face (present) , Abnormality of the ear (present) , Syndactyly (present) , Premature birth (present) , Talipes equinovarus (present) , Tongue thrusting (present) (less)
Method: Microarray
Result:
Pass
Observation 53:
Number of individuals with the variant: 1
Clinical Features:
Micrognathia (present) , Syndactyly (present) , Intrauterine growth retardation (present) , Ventricular septal defect (present) , Abnormal facial shape (present)
Sex: female
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 54:
Number of individuals with the variant: 1
Clinical Features:
Abnormality of the liver (present) , Intrauterine growth retardation (present) , Respiratory distress (present) , Sepsis (present)
Method: Microarray
Result:
Pass
Observation 55:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 56:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 57:
Number of individuals with the variant: 1
Clinical Features:
Low-set ears (present) , Muscular hypotonia (present) , Bilateral single transverse palmar creases (present)
Method: Microarray
Result:
Pass
Observation 58:
Number of individuals with the variant: 1
Clinical Features:
Epicanthus (present) , Short neck (present) , Upslanted palpebral fissure (present) , Muscular hypotonia (present) , Sandal gap (present)
Method: Microarray
Result:
Pass
Observation 59:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 60:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 61:
Number of individuals with the variant: 1
Clinical Features:
Microcephaly (present) , Webbed neck (present) , Thickened nuchal skin fold (present) , Muscular hypotonia (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 62:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 63:
Number of individuals with the variant: 1
Clinical Features:
Intrauterine growth retardation (present) , Premature birth (present) , Complete atrioventricular canal defect (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 64:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 65:
Number of individuals with the variant: 1
Clinical Features:
Abnormal facial shape (present)
Method: Microarray
Result:
Pass
Observation 66:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 67:
Number of individuals with the variant: 1
Clinical Features:
Atrial septal defect (present) , Duodenal atresia (present) , Abnormal facial shape (present)
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 68:
Number of individuals with the variant: 1
Clinical Features:
Abnormal heart morphology (present)
Method: Microarray
Result:
Pass
Observation 69:
Number of individuals with the variant: 1
Clinical Features:
Premature birth (present) , Abnormal heart morphology (present)
Method: Microarray
Result:
Pass
Observation 70:
Number of individuals with the variant: 1
Clinical Features:
Low-set ears (present) , Muscular hypotonia (present) , Atrial septal defect (present) , Abnormality of the pulmonary valve (present) , Patent foramen ovale (present)
Method: Microarray
Result:
Pass
Observation 71:
Number of individuals with the variant: 1
Clinical Features:
obsolete Malformation of the heart and great vessels (present)
Method: Microarray
Result:
Pass
Observation 72:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present) , Abnormal facial shape (present) , Wide intermamillary distance (present)
Method: Microarray
Result:
Pass
Observation 73:
Number of individuals with the variant: 1
Clinical Features:
Intrauterine growth retardation (present) , Abnormality of limb bone morphology (present)
Method: Microarray
Result:
Pass
Observation 74:
Number of individuals with the variant: 1
Clinical Features:
Hypospadias (present) , Thrombocytopenia (present) , Polycythemia (present) , Abnormal facial shape (present)
Method: Microarray
Result:
Pass
|
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Sep 01, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.