rs3734441

Positions:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001374828.1(ARID1B):c.2382G>A(p.Ala794=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,613,790 control chromosomes in the GnomAD database, including 219,781 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17741 hom., cov: 31)

Exomes 𝑓: 0.52 ( 202040 hom. )

Consequence

ARID1B
NM_001374828.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.618

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 6-157084796-G-A is Benign according to our data. Variant chr6-157084796-G-A is described in ClinVar as [Benign]. Clinvar id is 126320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-157084796-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.618 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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.2382G>A	p.Ala794=	synonymous_variant	5/20	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.2382G>A	p.Ala794=	synonymous_variant	5/20	2	NM_001374828.1	ENSP00000490491	A2	Q8NFD5-3

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71824

AN:

151786

Hom.:

17738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.683

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.499

GnomAD3 exomes

AF:

0.523

AC:

131459

AN:

251256

Hom.:

35194

AF XY:

0.527

AC XY:

71548

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.328

Gnomad AMR exome

AF:

0.610

Gnomad ASJ exome

AF:

0.608

Gnomad EAS exome

AF:

0.550

Gnomad SAS exome

AF:

0.566

Gnomad FIN exome

AF:

0.389

Gnomad NFE exome

AF:

0.527

Gnomad OTH exome

AF:

0.521

GnomAD4 exome

AF:

0.523

AC:

764659

AN:

1461886

Hom.:

202040

Cov.:

AF XY:

0.525

AC XY:

381655

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.333

Gnomad4 AMR exome

AF:

0.603

Gnomad4 ASJ exome

AF:

0.606

Gnomad4 EAS exome

AF:

0.571

Gnomad4 SAS exome

AF:

0.571

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.524

Gnomad4 OTH exome

AF:

0.520

GnomAD4 genome

AF:

0.473

AC:

71858

AN:

151904

Hom.:

17741

Cov.:

AF XY:

0.472

AC XY:

35011

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.340

Gnomad4 AMR

AF:

0.558

Gnomad4 ASJ

AF:

0.589

Gnomad4 EAS

AF:

0.553

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.524

Gnomad4 OTH

AF:

0.499

Alfa

AF:

0.526

Hom.:

39031

Bravo

AF:

0.479

Asia WGS

AF:

0.526

AC:

1831

AN:

3478

EpiCase

AF:

0.539

EpiControl

AF:

0.541

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Apr 25, 2013	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 13, 2016

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. -

Coffin-Siris syndrome 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.60

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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