rs10281879

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_021167.5(GATAD1):c.160G>A(p.Gly54Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,275,386 control chromosomes in the GnomAD database, including 8,931 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 871 hom., cov: 33)

Exomes 𝑓: 0.12 ( 8060 hom. )

Consequence

GATAD1
NM_021167.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.644

Variant links:

Genes affected

GATAD1 (HGNC:29941): (GATA zinc finger domain containing 1) The protein encoded by this gene contains a zinc finger at the N-terminus, and is thought to bind to a histone modification site that regulates gene expression. Mutations in this gene have been associated with autosomal recessive dilated cardiomyopathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]

GATAD1 links:

TMBIM7P (HGNC:49212): (transmembrane BAX inhibitor motif containing 7, pseudogene)

TMBIM7P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023853183).

BP6

Variant 7-92447889-G-A is Benign according to our data. Variant chr7-92447889-G-A is described in ClinVar as [Benign]. Clinvar id is 45825.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-92447889-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATAD1	NM_021167.5 link	c.160G>A	p.Gly54Ser	missense_variant	Exon 1 of 5	ENST00000287957.5	NP_066990.3	Q8WUU5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GATAD1	ENST00000287957.5 link	c.160G>A	p.Gly54Ser	missense_variant	Exon 1 of 5	1	NM_021167.5	ENSP00000287957.3	Q8WUU5
GATAD1	ENST00000644160.1 link	n.16G>A		non_coding_transcript_exon_variant	Exon 1 of 2
GATAD1	ENST00000645746.1 link	n.160G>A		non_coding_transcript_exon_variant	Exon 1 of 6			ENSP00000493785.1	A0A2R8Y4H1
TMBIM7P	ENST00000641474.1 link	n.-76C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15848

AN:

151870

Hom.:

873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0797

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0793

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0370

Gnomad SAS

AF:

0.0844

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.171

AC:

1200

AN:

7038

Hom.:

AF XY:

0.174

AC XY:

599

AN XY:

3448

show subpopulations

Gnomad AFR exome

AF:

0.385

Gnomad AMR exome

AF:

0.400

Gnomad ASJ exome

AF:

0.450

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.208

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.119

AC:

133478

AN:

1123410

Hom.:

8060

Cov.:

AF XY:

0.119

AC XY:

64158

AN XY:

537894

show subpopulations

Gnomad4 AFR exome

AF:

0.0814

Gnomad4 AMR exome

AF:

0.0883

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.0414

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.140

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.104

AC:

15852

AN:

151976

Hom.:

871

Cov.:

AF XY:

0.104

AC XY:

7694

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.0798

Gnomad4 AMR

AF:

0.0790

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.0371

Gnomad4 SAS

AF:

0.0847

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.119

Alfa

AF:

0.119

Hom.:

132

Bravo

AF:

0.101

TwinsUK

AF:

0.105

AC:

388

ALSPAC

AF:

0.118

AC:

454

ExAC

AF:

0.0869

AC:

765

Asia WGS

AF:

0.0780

AC:

270

AN:

3442

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Dilated cardiomyopathy 2B

Benign:4

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 28, 2017

Genome Diagnostics Laboratory, University Medical Center Utrecht

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

- -

Aug 01, 2017

Phosphorus, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:3

Mar 19, 2012

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Gly54Ser in Exon 01 of GATAD1: This variant is not expected to have clinical s ignificance because it has been identified in 9.4% (282/2994) of European Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs10281879). -

Nov 18, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Apr 10, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.090

CADD

Benign

DANN

Benign

0.90

DEOGEN2

Benign

0.0029

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.29

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.88

MutationAssessor

Benign

0.0

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

0.50

REVEL

Benign

0.23

Sift

Benign

0.71

Sift4G

Benign

0.16

Polyphen

0.0

Vest4

0.053

MPC

0.30

ClinPred

0.031

GERP RS

-1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

Varity_R

0.11

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