dbSNP rs1455234951: ARID1B:p.Gly410Glu (chr6-156778909-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.1229G>A(p.Gly410Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000829 in 1,205,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G410A) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 29)

Exomes 𝑓: 8.3e-7 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

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=0.16803104).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001374828.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ARID1B	NM_001374828.1	MANE Select	c.1229G>A	p.Gly410Glu	missense	Exon 1 of 20	NP_001361757.1
ARID1B	NM_001438482.1		c.1229G>A	p.Gly410Glu	missense	Exon 1 of 21	NP_001425411.1
ARID1B	NM_001438483.1		c.1229G>A	p.Gly410Glu	missense	Exon 1 of 21	NP_001425412.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ARID1B	ENST00000636930.2	TSL:2 MANE Select	c.1229G>A	p.Gly410Glu	missense	Exon 1 of 20	ENSP00000490491.2
ARID1B	ENST00000346085.10	TSL:1	c.1229G>A	p.Gly410Glu	missense	Exon 2 of 21	ENSP00000344546.5
ARID1B	ENST00000350026.11	TSL:1	c.1229G>A	p.Gly410Glu	missense	Exon 1 of 19	ENSP00000055163.8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.29e-7

AC:

AN:

1205832

Hom.:

Cov.:

AF XY:

0.00000170

AC XY:

AN XY:

588810

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23726

American (AMR)

AF:

0.00

AC:

AN:

11572

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17456

East Asian (EAS)

AF:

0.00

AC:

AN:

24416

South Asian (SAS)

AF:

0.00

AC:

AN:

47724

European-Finnish (FIN)

AF:

0.00

AC:

AN:

37478

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4010

European-Non Finnish (NFE)

AF:

0.00000101

AC:

AN:

990594

Other (OTH)

AF:

0.00

AC:

AN:

48856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_addAF

Benign

-0.074

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.89

DEOGEN2

Benign

0.015

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.29

M_CAP

Pathogenic

0.44

MetaRNN

Benign

0.17

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.0

PhyloP100

1.1

PrimateAI

Pathogenic

0.92

PROVEAN

Benign

-0.040

REVEL

Benign

0.057

Sift

Pathogenic

0.0

Sift4G

Benign

0.22

Polyphen

0.030

Vest4

0.36

MutPred

0.35

Loss of helix (P = 0.028)

MVP

0.10

MPC

0.38

ClinPred

0.35

GERP RS

1.9

PromoterAI

-0.22

Neutral

(source)

Varity_R

0.11

gMVP

0.21

Mutation Taster

=92/8

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over