8-11708563-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001308093.3(GATA4):ā€‹c.251A>Cā€‹(p.Gln84Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q84R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000016 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GATA4
NM_001308093.3 missense

Scores

4
4
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.86
Variant links:
Genes affected
GATA4 (HGNC:4173): (GATA binding protein 4) This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GATA4NM_001308093.3 linkuse as main transcriptc.251A>C p.Gln84Pro missense_variant 2/7 ENST00000532059.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GATA4ENST00000532059.6 linkuse as main transcriptc.251A>C p.Gln84Pro missense_variant 2/71 NM_001308093.3 A1P43694-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000162
AC:
2
AN:
1232410
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
601098
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000198
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.056
BayesDel_addAF
Pathogenic
0.22
D
BayesDel_noAF
Uncertain
0.080
CADD
Benign
22
DANN
Benign
0.52
DEOGEN2
Uncertain
0.63
D;.;.;T
Eigen
Benign
0.043
Eigen_PC
Benign
-0.0026
FATHMM_MKL
Benign
0.71
D
M_CAP
Pathogenic
0.98
D
MetaRNN
Uncertain
0.52
D;D;D;D
MetaSVM
Uncertain
0.69
D
MutationAssessor
Benign
1.4
L;.;L;.
MutationTaster
Benign
1.0
D;N;N
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
0.50
N;N;N;.
REVEL
Pathogenic
0.69
Sift
Benign
0.26
T;T;T;.
Sift4G
Benign
0.38
T;T;T;T
Polyphen
0.97
D;.;.;.
Vest4
0.51
MutPred
0.49
Gain of relative solvent accessibility (P = 0.0023);Gain of relative solvent accessibility (P = 0.0023);Gain of relative solvent accessibility (P = 0.0023);.;
MVP
0.90
MPC
0.094
ClinPred
0.45
T
GERP RS
3.4
Varity_R
0.24
gMVP
0.53

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.

Other links and lift over

dbSNP: rs899093640; hg19: chr8-11566072; API