Variant 6-156779262-G-GCGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBA1

The NM_001374828.1(ARID1B):c.1597_1599dupCCG(p.Pro533dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 1,145,648 control chromosomes in the GnomAD database, including 3,584 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 426 hom., cov: 28)

Exomes 𝑓: 0.077 ( 3158 hom. )

Consequence

ARID1B
NM_001374828.1 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.906

Variant links:

Genes affected

ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

ARID1B links:

ARID1B (HGNC:):

ARID1B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001374828.1

BP6

Variant 6-156779262-G-GCGC is Benign according to our data. Variant chr6-156779262-G-GCGC is described in ClinVar as [Benign]. Clinvar id is 126314.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID1B	NM_001374828.1 linkuse as main transcript	c.1597_1599dupCCG	p.Pro533dup	conservative_inframe_insertion	1/20	ENST00000636930.2	NP_001361757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID1B	ENST00000636930.2 linkuse as main transcript	c.1597_1599dupCCG	p.Pro533dup	conservative_inframe_insertion	1/20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.0644

AC:

9007

AN:

139838

Hom.:

426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0195

Gnomad AMI

AF:

0.0337

Gnomad AMR

AF:

0.0561

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.000221

Gnomad SAS

AF:

0.0247

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.0317

Gnomad NFE

AF:

0.0894

Gnomad OTH

AF:

0.0628

GnomAD3 exomes

AF:

0.0390

AC:

2531

AN:

64972

Hom.:

AF XY:

0.0400

AC XY:

1507

AN XY:

37640

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.0145

Gnomad ASJ exome

AF:

0.0264

Gnomad EAS exome

AF:

0.000365

Gnomad SAS exome

AF:

0.0153

Gnomad FIN exome

AF:

0.0902

Gnomad NFE exome

AF:

0.0532

Gnomad OTH exome

AF:

0.0572

GnomAD4 exome

AF:

0.0765

AC:

76940

AN:

1005698

Hom.:

3158

Cov.:

AF XY:

0.0752

AC XY:

36108

AN XY:

480220

show subpopulations

Gnomad4 AFR exome

AF:

0.0165

Gnomad4 AMR exome

AF:

0.0175

Gnomad4 ASJ exome

AF:

0.0302

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.0250

Gnomad4 FIN exome

AF:

0.0768

Gnomad4 NFE exome

AF:

0.0833

Gnomad4 OTH exome

AF:

0.0617

GnomAD4 genome

AF:

0.0644

AC:

9008

AN:

139950

Hom.:

426

Cov.:

AF XY:

0.0666

AC XY:

4538

AN XY:

68106

show subpopulations

Gnomad4 AFR

AF:

0.0195

Gnomad4 AMR

AF:

0.0560

Gnomad4 ASJ

AF:

0.0395

Gnomad4 EAS

AF:

0.000222

Gnomad4 SAS

AF:

0.0249

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.0894

Gnomad4 OTH

AF:

0.0622

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 11, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jan 24, 2014

- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 21, 2017

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over