chr8-11758367-A-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001308093.3(GATA4):āc.1224A>Cā(p.Pro408=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000732 in 1,614,000 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P408P) has been classified as Likely benign.
Frequency
Consequence
NM_001308093.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA4 | NM_001308093.3 | c.1224A>C | p.Pro408= | synonymous_variant | 7/7 | ENST00000532059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA4 | ENST00000532059.6 | c.1224A>C | p.Pro408= | synonymous_variant | 7/7 | 1 | NM_001308093.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00393 AC: 597AN: 152002Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000799 AC: 201AN: 251472Hom.: 1 AF XY: 0.000596 AC XY: 81AN XY: 135916
GnomAD4 exome AF: 0.000397 AC: 581AN: 1461880Hom.: 8 Cov.: 31 AF XY: 0.000331 AC XY: 241AN XY: 727238
GnomAD4 genome AF: 0.00395 AC: 601AN: 152120Hom.: 1 Cov.: 32 AF XY: 0.00362 AC XY: 269AN XY: 74352
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 01, 2018 | - - |
Atrioventricular septal defect 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 02, 2021 | This variant is associated with the following publications: (PMID: 18055909) - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at