Genetic Variant NM_021167.5:c.31G>T (chr7-92447760-G-T) – 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_021167.5(GATAD1):c.31G>T(p.Val11Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000743 in 1,346,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. V11I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 7.4e-7 ( 0 hom. )

Consequence

GATAD1
NM_021167.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.63

Publications

0 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:

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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=0.2509632).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATAD1	NM_021167.5 link	c.31G>T	p.Val11Leu	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.31G>T	p.Val11Leu	missense_variant	Exon 1 of 5	1	NM_021167.5	ENSP00000287957.3	Q8WUU5
TMBIM7P	ENST00000641474.1 link	n.54C>A		non_coding_transcript_exon_variant	Exon 1 of 10
GATAD1	ENST00000645746.1 link	n.31G>T		non_coding_transcript_exon_variant	Exon 1 of 6			ENSP00000493785.1	A0A2R8Y4H1
GATAD1	ENST00000644160.1 link	n.-114G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

7.43e-7

AC:

AN:

1346720

Hom.:

Cov.:

AF XY:

0.00000151

AC XY:

AN XY:

664318

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26864

American (AMR)

AF:

0.00

AC:

AN:

28910

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23496

East Asian (EAS)

AF:

0.00

AC:

AN:

28480

South Asian (SAS)

AF:

0.00

AC:

AN:

75172

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47228

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5552

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1055630

Other (OTH)

AF:

0.0000181

AC:

AN:

55388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Uncertain

0.035

BayesDel_noAF

Benign

-0.19

CADD

Benign

(source)

DANN

Benign

0.80

DEOGEN2

Benign

0.0067

Eigen

Benign

-0.54

Eigen_PC

Benign

-0.41

FATHMM_MKL

Benign

0.69

LIST_S2

Benign

0.82

M_CAP

Pathogenic

0.96

MetaRNN

Benign

0.25

MetaSVM

Uncertain

0.78

MutationAssessor

Benign

0.81

PhyloP100

3.6

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-0.030

REVEL

Uncertain

0.33

Sift

Benign

0.32

Sift4G

Benign

0.79

Polyphen

0.0040

Vest4

0.22

MutPred

0.23

Loss of sheet (P = 0.0357);

MVP

0.23

MPC

0.31

ClinPred

0.14

GERP RS

2.6

PromoterAI

0.034

Neutral

(source)

Varity_R

0.053

gMVP

0.21

Mutation Taster

=85/15

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

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NM_021167.5:c.31G>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over