chr7-92447889-G-A

Position:

chr7-92447889-G-A

Variant summary

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

The ENST00000287957.5(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 (★★). 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
ENST00000287957.5 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:

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/exons	MANE	Protein	UniProt
GATAD1	NM_021167.5 linkuse as main transcript	c.160G>A	p.Gly54Ser	missense_variant	1/5	ENST00000287957.5	NP_066990.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
GATAD1	ENST00000287957.5 linkuse as main transcript	c.160G>A	p.Gly54Ser	missense_variant	1/5	1	NM_021167.5	ENSP00000287957	P1
GATAD1	ENST00000644160.1 linkuse as main transcript	n.16G>A		non_coding_transcript_exon_variant	1/2
GATAD1	ENST00000645746.1 linkuse as main transcript	c.160G>A	p.Gly54Ser	missense_variant, NMD_transcript_variant	1/6			ENSP00000493785

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

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Phosphorus, Inc.	Aug 01, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Jul 28, 2017	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 18, 2013	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. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 19, 2012	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). -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 10, 2015	- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

MutationTaster

Benign

1.0

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