VCV000931777.9 - ClinVar

NM_001374828.1(ARID1B):c.1638_1647del (p.Ala547fs)

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.

(5)

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.1638_1647del (p.Ala547fs)

Variation ID: 931777 Accession: VCV000931777.9

Type and length

Deletion, 10 bp

Location

Cytogenetic: 6q25.3 6: 156779311-156779320 (GRCh38) [ NCBI UCSC ] 6: 157100445-157100454 (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	Jul 4, 2020	May 27, 2023	May 16, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001374828.1:c.1638_1647del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001361757.1:p.Ala547fs	frameshift
NM_001371656.1:c.1638_1647del	NP_001358585.1:p.Ala547fs	frameshift
NM_001374820.1:c.1638_1647del	NP_001361749.1:p.Ala547fs	frameshift
NM_017519.3:c.1638_1647del	NP_059989.3:p.Ala547fs	frameshift
NM_020732.3:c.1389_1398del
NM_020732.3:c.1389_1398del10
NM_020732.3:c.1389_1398delGGCGGGCGGC
NC_000006.12:g.156779318_156779327del
NC_000006.11:g.157100452_157100461del
NG_066624.1:g.8293_8302del
NG_109547.2:g.824_833del

... more HGVS ... less HGVS

Protein change

A547fs

Other names

Canonical SPDI

NC_000006.12:156779310:GGGCGGCGGCGGGCGGC:GGGCGGC

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

dbSNP: rs1131691339 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	1899	2251

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	Pathogenic (2)	criteria provided, multiple submitters, no conflicts	Jul 15, 2021	RCV001198668.4
ARID1B-related BAFopathy	Pathogenic (1)	criteria provided, single submitter	Jun 10, 2021	RCV001533083.1
Inborn genetic diseases	Pathogenic (1)	criteria provided, single submitter	Nov 28, 2017	RCV001265674.2
not provided	Pathogenic (1)	criteria provided, single submitter	May 16, 2023	RCV003229021.1

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 (Oct 22, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Coffin-Siris syndrome 1 Affected status: yes Allele origin: unknown	Centre for Mendelian Genomics, University Medical Centre Ljubljana Accession: SCV001369663.2 First in ClinVar: Jul 04, 2020 Last updated: Jul 04, 2020	Comment: This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP4.
Pathogenic (Jun 10, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	ARID1B-related BAFopathy Affected status: yes Allele origin: de novo	Baylor Genetics Accession: SCV001748903.1 First in ClinVar: Jul 10, 2021 Last updated: Jul 10, 2021
Pathogenic (Jul 15, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Coffin-Siris syndrome 1 Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV002054265.1 First in ClinVar: Jan 12, 2022 Last updated: Jan 12, 2022
Pathogenic (Nov 28, 2017)	criteria provided, single submitter (Ambry exome assertion method (8-5-2015)) Method: clinical testing	Inborn genetic diseases Affected status: yes Allele origin: germline	Ambry Genetics Accession: SCV001443841.2 First in ClinVar: Nov 21, 2020 Last updated: Jan 07, 2023	Publications: PubMed (1) PubMed: 23815551 Number of individuals with the variant: 1 Sex: female Ethnicity/Population group: Caucasian
Pathogenic (May 16, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003925995.1 First in ClinVar: May 27, 2023 Last updated: May 27, 2023	Comment: Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more) Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23815551, 30349098) (less)

Comment:

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23815551, 30349098)

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
Coffin-Siris syndrome is a SWI/SNF complex disorder.	Tsurusaki Y	Clinical genetics	2014	PMID: 23815551

Text-mined citations for rs1131691339 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

NM_001374828.1(ARID1B):c.1638_1647del (p.Ala547fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1131691339 ...