chr7-92447886-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000287957.5(GATAD1):āc.157G>Cā(p.Gly53Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,278,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G53W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000287957.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATAD1 | NM_021167.5 | c.157G>C | p.Gly53Arg | missense_variant | 1/5 | ENST00000287957.5 | NP_066990.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATAD1 | ENST00000287957.5 | c.157G>C | p.Gly53Arg | missense_variant | 1/5 | 1 | NM_021167.5 | ENSP00000287957 | P1 | |
GATAD1 | ENST00000644160.1 | n.13G>C | non_coding_transcript_exon_variant | 1/2 | ||||||
GATAD1 | ENST00000645746.1 | c.157G>C | p.Gly53Arg | missense_variant, NMD_transcript_variant | 1/6 | ENSP00000493785 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151936Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000231 AC: 26AN: 1126978Hom.: 0 Cov.: 30 AF XY: 0.0000204 AC XY: 11AN XY: 539858
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151936Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74234
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 2B Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 23, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 18, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 53 of the GATAD1 protein (p.Gly53Arg). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with GATAD1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2019 | The p.G53R variant (also known as c.157G>C), located in coding exon 1 of the GATAD1 gene, results from a G to C substitution at nucleotide position 157. The glycine at codon 53 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at