VCV003236222.1 - ClinVar

NM_001374828.1(ARID1B):c.6451_6453del (p.Leu2151del)

Germline

Classification

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.

(1)

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001374828.1(ARID1B):c.6451_6453del (p.Leu2151del)

Variation ID: 3236222 Accession: VCV003236222.1

Type and length

Deletion, 3 bp

Location

Cytogenetic: 6q25.3 6: 157207222-157207224 (GRCh38) [ NCBI UCSC ] 6: 157528356-157528358 (GRCh37) [ 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	May 19, 2024	May 19, 2024	May 22, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001374828.1:c.6451_6453del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001361757.1:p.Leu2151del	inframe deletion
NM_001346813.1:c.6202_6204delTTG	NP_001333742.1:p.Leu2068del	inframe indel
NM_001363725.2:c.3952_3954del	NP_001350654.1:p.Leu1318del	inframe deletion
NM_001371656.1:c.6331_6333del	NP_001358585.1:p.Leu2111del	inframe deletion
NM_001374820.1:c.6331_6333del	NP_001361749.1:p.Leu2111del	inframe deletion
NM_017519.3:c.6292_6294del	NP_059989.3:p.Leu2098del	inframe deletion
NM_020732.3:c.6082_6084delTTG	NP_065783.3:p.Leu2028del	inframe indel
NM_175863.2:c.5869_5871delTTG	NP_787059.2:p.Leu1957del	inframe indel
NC_000006.12:g.157207223_157207225del
NC_000006.11:g.157528357_157528359del
NG_066624.1:g.436198_436200del
NG_109565.1:g.333_335del

... more HGVS ... less HGVS

Protein change

L1318del, L1957del, L2028del, L2068del, L2098del, L2111del, L2151del

Other names

Canonical SPDI

NC_000006.12:157207221:GTTG:G

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ARID1B		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1881	2231

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.
Coffin-Siris syndrome 1	Likely pathogenic (1)	criteria provided, single submitter	May 22, 2023	RCV004555478.2

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.
Likely pathogenic (May 22, 2023)	criteria provided, single submitter (UK Practice Guidelines For Variant Classification V4 01 2020) Method: clinical testing	Coffin-Siris syndrome 1 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	MVZ Medizinische Genetik Mainz Accession: SCV005044453.1 First in ClinVar: May 19, 2024 Last updated: May 19, 2024	Comment: ACMG Criteria: PS2,PM4,PM2_SUP,PP3,PP4,BP1 Number of individuals with the variant: 1 Clinical Features: Cryptorchidism (present) , High palate (present) , Low anterior hairline (present) , Triangular face (present) , Abnormal eyebrow morphology (present) , Hypertrichosis (present) , Global … (more) Cryptorchidism (present) , High palate (present) , Low anterior hairline (present) , Triangular face (present) , Abnormal eyebrow morphology (present) , Hypertrichosis (present) , Global developmental delay (present) , Aplasia/Hypoplasia of toe (present) , Constipation (present) , Hypoplasia of the radius (present) , Congenital laryngeal stridor (present) , Aplasia/Hypoplasia of the 5th finger (present) , Horizontal eyebrow (present) (less)

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

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 ...

Record last updated Jun 02, 2024

ClinVar Genomic variation as it relates to human health

NM_001374828.1(ARID1B):c.6451_6453del (p.Leu2151del)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...