dbSNP rs587779740: ARID1B:p.Ala542Thr (chr6-156779304-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001374828.1(ARID1B):c.1624G>A(p.Ala542Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ARID1B
NM_001374828.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.796

Publications

0 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:

ENSG00000296922 (HGNC:):

ENSG00000296922 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.118282914).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.1624G>A	p.Ala542Thr	missense_variant	Exon 1 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.1624G>A	p.Ala542Thr	missense_variant	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

990860

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

468168

African (AFR)

AF:

0.00

AC:

AN:

19388

American (AMR)

AF:

0.00

AC:

AN:

5416

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10132

East Asian (EAS)

AF:

0.00

AC:

AN:

18612

South Asian (SAS)

AF:

0.00

AC:

AN:

18758

European-Finnish (FIN)

AF:

0.00

AC:

AN:

16076

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2448

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

863252

Other (OTH)

AF:

0.00

AC:

AN:

36778

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Coffin Siris/Intellectual Disability

Uncertain:1

Jul 08, 2013

Genetic Services Laboratory, University of Chicago

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Benign

-0.55

CADD

Uncertain

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.014

.;T;.;.

Eigen

Benign

-0.78

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.52

T;T;T;T

M_CAP

Uncertain

0.13

MetaRNN

Benign

0.12

T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.0

.;N;N;N

PhyloP100

0.80

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-0.50

.;N;.;.

REVEL

Benign

0.017

Sift

Benign

0.043

.;D;.;.

Sift4G

Uncertain

0.028

.;D;.;.

Polyphen

0.057, 0.094

.;B;.;B

Vest4

0.14

MutPred

0.35

.;Gain of glycosylation at A459 (P = 0.0036);Gain of glycosylation at A459 (P = 0.0036);Gain of glycosylation at A459 (P = 0.0036);

MVP

0.14

MPC

0.29

ClinPred

0.095

GERP RS

1.5

PromoterAI

-0.0065

Neutral

(source)

Varity_R

0.12

gMVP

0.21

Mutation Taster

=95/5

polymorphism

(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

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over