VCV002502041.2 - ClinVar

NM_001374828.1(ARID1B):c.5916del (p.Pro1972_Leu1973insTer)

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.

(2)

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.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001374828.1(ARID1B):c.5916del (p.Pro1972_Leu1973insTer)

Variation ID: 2502041 Accession: VCV002502041.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 6q25.3 6: 157206683 (GRCh38) [ NCBI UCSC ] 6: 157527817 (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 20, 2023	Oct 21, 2023	Nov 11, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001374828.1:c.5916del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001361757.1:p.Pro1972_Leu1973insTer	frameshift
NM_001363725.2:c.3417del	NP_001350654.1:p.Pro1139_Leu1140insTer	frameshift
NM_001371656.1:c.5796del	NP_001358585.1:p.Pro1932_Leu1933insTer	frameshift
NM_001374820.1:c.5796del	NP_001361749.1:p.Pro1932_Leu1933insTer	frameshift
NM_017519.3:c.5757del	NP_059989.3:p.Pro1919_Leu1920insTer	frameshift
NM_020732.3:c.5547del		frameshift nonsense
NC_000006.12:g.157206688del
NC_000006.11:g.157527822del
NG_066624.1:g.435663del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000006.12:157206682:CCCCCC:CCCCC

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.
not provided	Pathogenic (1)	criteria provided, single submitter	Nov 11, 2022	RCV003228460.1
ARID1B-related disorder	Pathogenic (1)	criteria provided, single submitter	-	RCV003336836.1

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.
Pathogenic (Nov 11, 2022)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003924860.1 First in ClinVar: May 20, 2023 Last updated: May 20, 2023	Comment: Nonsense variant predicted to result in protein truncation, as the last 400 amino acids are lost, and other loss-of-function variants have been reported downstream in … (more) Nonsense variant predicted to result in protein truncation, as the last 400 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34217350, 31069529) (less)
Pathogenic (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	ARID1B-Related Disorder Affected status: yes Allele origin: germline	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego Accession: SCV004046033.1 First in ClinVar: Oct 21, 2023 Last updated: Oct 21, 2023	Comment: This frameshift variant is found in the last exon of ARID1B and is predicted to escape nonsense-mediated mRNA decay (NMD). However, frameshift and nonsense variants … (more) This frameshift variant is found in the last exon of ARID1B and is predicted to escape nonsense-mediated mRNA decay (NMD). However, frameshift and nonsense variants located downstream of this variant have been reported in the literature in patients with ARID1B-related phenotypes (PMID: 30349098, 31273213). The c.5547del (p.Leu1850Ter) variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the gnomAD population database and thus presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.5547del (p.Leu1850Ter) variant is classified as Pathogenic. (less)

Comment:

Nonsense variant predicted to result in protein truncation, as the last 400 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34217350, 31069529)

Comment:

This frameshift variant is found in the last exon of ARID1B and is predicted to escape nonsense-mediated mRNA decay (NMD). However, frameshift and nonsense variants located downstream of this variant have been reported in the literature in patients with ARID1B-related phenotypes (PMID: 30349098, 31273213). The c.5547del (p.Leu1850Ter) variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the gnomAD population database and thus presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.5547del (p.Leu1850Ter) variant is classified as Pathogenic.

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

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 Sep 01, 2024

ClinVar Genomic variation as it relates to human health

NM_001374828.1(ARID1B):c.5916del (p.Pro1972_Leu1973insTer)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...