rs10281879

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G54D) has been classified as Uncertain significance.

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

Publications

13 publications found

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 Gene-Disease associations (from GenCC):

familial isolated dilated cardiomyopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
dilated cardiomyopathy
Inheritance: AR Classification: LIMITED Submitted by: ClinGen
dilated cardiomyopathy 2B
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

GATAD1 links:

TMBIM7P (HGNC:):

TMBIM7P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 45825.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

GnomAD2 exomes

AF:

0.171

AC:

1200

AN:

7038

AF XY:

0.174

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 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

African (AFR)

AF:

0.0814

AC:

1856

AN:

22812

American (AMR)

AF:

0.0883

AC:

734

AN:

8310

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

2019

AN:

14428

East Asian (EAS)

AF:

0.0414

AC:

1084

AN:

26180

South Asian (SAS)

AF:

0.126

AC:

3365

AN:

26748

European-Finnish (FIN)

AF:

0.140

AC:

4584

AN:

32642

Middle Eastern (MID)

AF:

0.125

AC:

501

AN:

4018

European-Non Finnish (NFE)

AF:

0.121

AC:

114013

AN:

943340

Other (OTH)

AF:

0.118

AC:

5322

AN:

44932

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

6542

13084

19625

26167

32709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4560

9120

13680

18240

22800

<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:

0.104

AC:

15852

AN:

151976

Hom.:

871

Cov.:

AF XY:

0.104

AC XY:

7694

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0798

AC:

3313

AN:

41502

American (AMR)

AF:

0.0790

AC:

1206

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

478

AN:

3468

East Asian (EAS)

AF:

0.0371

AC:

192

AN:

5178

South Asian (SAS)

AF:

0.0847

AC:

409

AN:

4830

European-Finnish (FIN)

AF:

0.130

AC:

1373

AN:

10530

Middle Eastern (MID)

AF:

0.123

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.125

AC:

8492

AN:

67898

Other (OTH)

AF:

0.119

AC:

251

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

748

1496

2245

2993

3741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.119

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

Aug 01, 2017

Phosphorus, Inc.

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

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

- -

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

(source)

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

PhyloP100

0.64

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

PromoterAI

0.024

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

Varity_R

0.11

gMVP

0.13

Mutation Taster

=91/9

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