rs200167770
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001308093.3(GATA4):āc.1067C>Gā(p.Thr356Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,614,272 control chromosomes in the GnomAD database, including 4 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. T356T) has been classified as Likely benign.
Frequency
Consequence
NM_001308093.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA4 | NM_001308093.3 | c.1067C>G | p.Thr356Ser | missense_variant | 6/7 | ENST00000532059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA4 | ENST00000532059.6 | c.1067C>G | p.Thr356Ser | missense_variant | 6/7 | 1 | NM_001308093.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152276Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00107 AC: 269AN: 251448Hom.: 4 AF XY: 0.00153 AC XY: 208AN XY: 135910
GnomAD4 exome AF: 0.000520 AC: 760AN: 1461878Hom.: 4 Cov.: 32 AF XY: 0.000782 AC XY: 569AN XY: 727240
GnomAD4 genome AF: 0.000289 AC: 44AN: 152394Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74522
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Atrioventricular septal defect 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at