6-157084796-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001374828.1(ARID1B):c.2382G>A(p.Ala794Ala) 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

Publications

23 publications found

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 Gene-Disease associations (from GenCC):

Coffin-Siris syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina, ClinGen
Coffin-Siris syndrome 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ARID1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 126320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.2382G>A	p.Ala794Ala	synonymous_variant	Exon 5 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.2382G>A	p.Ala794Ala	synonymous_variant	Exon 5 of 20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

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

GnomAD2 exomes

AF:

0.523

AC:

131459

AN:

251256

AF XY:

0.527

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 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

African (AFR)

AF:

0.333

AC:

11165

AN:

33480

American (AMR)

AF:

0.603

AC:

26986

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

15845

AN:

26136

East Asian (EAS)

AF:

0.571

AC:

22668

AN:

39698

South Asian (SAS)

AF:

0.571

AC:

49228

AN:

86258

European-Finnish (FIN)

AF:

0.392

AC:

20942

AN:

53420

Middle Eastern (MID)

AF:

0.549

AC:

3168

AN:

5768

European-Non Finnish (NFE)

AF:

0.524

AC:

583242

AN:

1112006

Other (OTH)

AF:

0.520

AC:

31415

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

24334

48668

73002

97336

121670

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16732

33464

50196

66928

83660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.473

AC:

71858

AN:

151904

Hom.:

17741

Cov.:

AF XY:

0.472

AC XY:

35011

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.340

AC:

14086

AN:

41420

American (AMR)

AF:

0.558

AC:

8533

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.589

AC:

2045

AN:

3472

East Asian (EAS)

AF:

0.553

AC:

2844

AN:

5144

South Asian (SAS)

AF:

0.584

AC:

2802

AN:

4794

European-Finnish (FIN)

AF:

0.386

AC:

4074

AN:

10550

Middle Eastern (MID)

AF:

0.610

AC:

178

AN:

292

European-Non Finnish (NFE)

AF:

0.524

AC:

35625

AN:

67924

Other (OTH)

AF:

0.499

AC:

1051

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1882

3764

5646

7528

9410

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.517

Hom.:

82707

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

Apr 25, 2013

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not provided

Benign:2

Jul 05, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Inborn genetic diseases

Benign:1

Mar 13, 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 14, 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

-0.80

CADD

Benign

0.60

(source)

DANN

Benign

0.62

PhyloP100

-0.62

PromoterAI

-0.012

Neutral

(source)

Mutation Taster

=76/24

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over