Variant 2-96551109-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_212481.3(ARID5A):c.581G>A(p.Gly194Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00594 in 1,611,098 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0061 ( 47 hom. )

Consequence

ARID5A
NM_212481.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.131

Variant links:

Genes affected

ARID5A (HGNC:17361): (AT-rich interaction domain 5A) Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).[supplied by OMIM, Mar 2008]

ARID5A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030888617).

BP6

Variant 2-96551109-G-A is Benign according to our data. Variant chr2-96551109-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041614.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID5A	NM_212481.3 linkuse as main transcript	c.581G>A	p.Gly194Glu	missense_variant	7/7	ENST00000357485.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID5A	ENST00000357485.8 linkuse as main transcript	c.581G>A	p.Gly194Glu	missense_variant	7/7	1	NM_212481.3	P1	Q03989-1

Frequencies

GnomAD3 genomes

AF:

0.00440

AC:

669

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.00222

Gnomad ASJ

AF:

0.000866

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00706

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00690

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00431

AC:

1070

AN:

248524

Hom.:

AF XY:

0.00435

AC XY:

585

AN XY:

134488

show subpopulations

Gnomad AFR exome

AF:

0.00117

Gnomad AMR exome

AF:

0.00143

Gnomad ASJ exome

AF:

0.000611

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00440

Gnomad FIN exome

AF:

0.00640

Gnomad NFE exome

AF:

0.00635

Gnomad OTH exome

AF:

0.00215

GnomAD4 exome

AF:

0.00610

AC:

8905

AN:

1458792

Hom.:

Cov.:

AF XY:

0.00602

AC XY:

4369

AN XY:

725596

show subpopulations

Gnomad4 AFR exome

AF:

0.000990

Gnomad4 AMR exome

AF:

0.00142

Gnomad4 ASJ exome

AF:

0.000695

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00409

Gnomad4 FIN exome

AF:

0.00576

Gnomad4 NFE exome

AF:

0.00708

Gnomad4 OTH exome

AF:

0.00428

GnomAD4 genome

AF:

0.00438

AC:

667

AN:

152306

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

326

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.000866

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.00706

Gnomad4 NFE

AF:

0.00690

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00581

Hom.:

Bravo

AF:

0.00385

TwinsUK

AF:

0.00944

AC:

ALSPAC

AF:

0.00727

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00709

AC:

ExAC

AF:

0.00431

AC:

523

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00557

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

ARID5A-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 29, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.54

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.013

T;.

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.63

T;T

M_CAP

Benign

0.020

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.8

L;.

MutationTaster

Benign

0.75

D;D

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.74

N;N

REVEL

Benign

0.028

Sift

Benign

0.092

T;T

Sift4G

Benign

0.95

T;T

Polyphen

0.0090

B;.

Vest4

0.047

MVP

0.30

MPC

0.19

ClinPred

0.0081

GERP RS

-1.7

Varity_R

0.052

gMVP

0.13

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