rs78253128

Positions:

chr6-156778292-A-G

Variant summary

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

The NM_001374828.1(ARID1B):c.612A>G(p.Gln204Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00432 in 1,517,812 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. QQ204Q?) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0048 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0043 ( 6 hom. )

Consequence

ARID1B
NM_001374828.1 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.113

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:

ENSG00000271551 (HGNC:):

ENSG00000271551 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=-0.82).

BP6

Variant 6-156778292-A-G is Benign according to our data. Variant chr6-156778292-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 126328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.113 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00482 (701/145396) while in subpopulation AFR AF= 0.00571 (208/36448). AF 95% confidence interval is 0.00507. There are 1 homozygotes in gnomad4. There are 353 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 701 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID1B	NM_001374828.1 linkuse as main transcript	c.612A>G	p.Gln204Gln	synonymous_variant	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.612A>G	p.Gln204Gln	synonymous_variant	1/20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.00482

AC:

701

AN:

145296

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00572

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00508

Gnomad ASJ

AF:

0.00117

Gnomad EAS

AF:

0.000605

Gnomad SAS

AF:

0.000419

Gnomad FIN

AF:

0.00737

Gnomad MID

AF:

0.00327

Gnomad NFE

AF:

0.00484

Gnomad OTH

AF:

0.00250

GnomAD3 exomes

AF:

0.00422

AC:

533

AN:

126374

Hom.:

AF XY:

0.00401

AC XY:

272

AN XY:

67906

show subpopulations

Gnomad AFR exome

AF:

0.00552

Gnomad AMR exome

AF:

0.00320

Gnomad ASJ exome

AF:

0.00143

Gnomad EAS exome

AF:

0.000531

Gnomad SAS exome

AF:

0.000576

Gnomad FIN exome

AF:

0.0105

Gnomad NFE exome

AF:

0.00582

Gnomad OTH exome

AF:

0.00745

GnomAD4 exome

AF:

0.00426

AC:

5851

AN:

1372416

Hom.:

Cov.:

AF XY:

0.00410

AC XY:

2779

AN XY:

677496

show subpopulations

Gnomad4 AFR exome

AF:

0.00537

Gnomad4 AMR exome

AF:

0.00382

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.000892

Gnomad4 SAS exome

AF:

0.000726

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.00446

Gnomad4 OTH exome

AF:

0.00430

GnomAD4 genome

AF:

0.00482

AC:

701

AN:

145396

Hom.:

Cov.:

AF XY:

0.00496

AC XY:

353

AN XY:

71142

show subpopulations

Gnomad4 AFR

AF:

0.00571

Gnomad4 AMR

AF:

0.00507

Gnomad4 ASJ

AF:

0.00117

Gnomad4 EAS

AF:

0.000607

Gnomad4 SAS

AF:

0.000419

Gnomad4 FIN

AF:

0.00737

Gnomad4 NFE

AF:

0.00484

Gnomad4 OTH

AF:

0.00248

Alfa

AF:

0.00780

Hom.:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 04, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jan 17, 2014

- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 05, 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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.5

DANN

Benign

0.80

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