rs61738955

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001374828.1(ARID1B):c.5001G>A(p.Pro1667Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 1,613,808 control chromosomes in the GnomAD database, including 1,059 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 76 hom., cov: 32)

Exomes 𝑓: 0.035 ( 983 hom. )

Consequence

ARID1B
NM_001374828.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.81

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 6-157201226-G-A is Benign according to our data. Variant chr6-157201226-G-A is described in ClinVar as [Benign]. Clinvar id is 126334.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.81 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0277 (4222/152232) while in subpopulation NFE AF= 0.0388 (2642/68010). AF 95% confidence interval is 0.0376. There are 76 homozygotes in gnomad4. There are 2005 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 4222 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.5001G>A	p.Pro1667Pro	synonymous_variant	Exon 18 of 20	ENST00000636930.2	NP_001361757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID1B	ENST00000636930.2 link	c.5001G>A	p.Pro1667Pro	synonymous_variant	Exon 18 of 20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.0278

AC:

4226

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00746

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.0355

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0118

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.0311

GnomAD3 exomes

AF:

0.0277

AC:

6955

AN:

251138

Hom.:

130

AF XY:

0.0280

AC XY:

3802

AN XY:

135736

show subpopulations

Gnomad AFR exome

AF:

0.00658

Gnomad AMR exome

AF:

0.0233

Gnomad ASJ exome

AF:

0.0339

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0132

Gnomad FIN exome

AF:

0.0372

Gnomad NFE exome

AF:

0.0380

Gnomad OTH exome

AF:

0.0295

GnomAD4 exome

AF:

0.0355

AC:

51856

AN:

1461576

Hom.:

983

Cov.:

AF XY:

0.0351

AC XY:

25494

AN XY:

727038

show subpopulations

Gnomad4 AFR exome

AF:

0.00672

Gnomad4 AMR exome

AF:

0.0231

Gnomad4 ASJ exome

AF:

0.0345

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0136

Gnomad4 FIN exome

AF:

0.0345

Gnomad4 NFE exome

AF:

0.0401

Gnomad4 OTH exome

AF:

0.0310

GnomAD4 genome

AF:

0.0277

AC:

4222

AN:

152232

Hom.:

Cov.:

AF XY:

0.0269

AC XY:

2005

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00744

Gnomad4 AMR

AF:

0.0367

Gnomad4 ASJ

AF:

0.0355

Gnomad4 EAS

AF:

0.000581

Gnomad4 SAS

AF:

0.0122

Gnomad4 FIN

AF:

0.0322

Gnomad4 NFE

AF:

0.0388

Gnomad4 OTH

AF:

0.0308

Alfa

AF:

0.0342

Hom.:

Bravo

AF:

0.0286

Asia WGS

AF:

0.00837

AC:

AN:

3478

EpiCase

AF:

0.0403

EpiControl

AF:

0.0444

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 07, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

May 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn genetic diseases

Benign:1

Apr 15, 2016

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

1.7

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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