VCV000694460.2 - ClinVar

NC_000009.11:g.12246100_101559378inv

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000009.11:g.12246100_101559378inv

Variation ID: 694460 Accession: VCV000694460.2

Type and length

Inversion, 89,313,279 bp

Location

Cytogenetic: 9p23-q22.33 9: 12246100-101559378 (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	Feb 3, 2020	Feb 3, 2020	Jul 5, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_000009.11:g.12246100_101559378inv

Protein change

Other names

Canonical SPDI

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.
CDKN2A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1261	1413
HNRNPK		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	161	276
PTCH1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	4021	5233
ELAVL2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	21	96
MTAP		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	164	251
PAX5		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	157	262
PHF2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	99	134
CENPP		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	19	173
FREM1		No evidence available	No evidence available	GRCh38 GRCh37	897	1047
ROR2		No evidence available	No evidence available	GRCh38 GRCh37	683	723

There are 318 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) 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.
Abnormal chromosome morphology Recurrent spontaneous abortion	Likely pathogenic (1)	no assertion criteria provided	Jul 5, 2019	RCV000999471.2

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 (Jul 05, 2019)	no assertion criteria provided Method: clinical testing	Recurrent spontaneous abortion Abnormal chromosome morphology Affected status: no Allele origin: germline	Cytogenetics and Genomics Lab, Cyprus Institute Of Neurology and Genetics Accession: SCV000999022.1 First in ClinVar: Feb 03, 2020 Last updated: Feb 03, 2020	Publications: PubMed (1) PubMed: 32398760 Comment: Large heterozygous pericentric inversion resulting in miscarriages, gross chromosomal abnormalities (recombinant chromosomes) and possibly infertility. The reported inversion can cause recurrent miscarriages due to the … (more) Large heterozygous pericentric inversion resulting in miscarriages, gross chromosomal abnormalities (recombinant chromosomes) and possibly infertility. The reported inversion can cause recurrent miscarriages due to the recombinant chromosomes that can be formed during meiosis. (less) Number of individuals with the variant: 30 Age: 2-50 years Sex: mixed Ethnicity/Population group: Caucasian Geographic origin: East Europe

Comment:

Large heterozygous pericentric inversion resulting in miscarriages, gross chromosomal abnormalities (recombinant chromosomes) and possibly infertility. The reported inversion can cause recurrent miscarriages due to the recombinant chromosomes that can be formed during meiosis.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Novel pericentric inversion inv(9)(p23q22.3) in unrelated individuals with fertility problems in the Southeast European population.	Sismani C	Journal of human genetics	2020	PMID: 32398760

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

NC_000009.11:g.12246100_101559378inv

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...