1-1522810-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001170535.3(ATAD3A):c.817C>T(p.Arg273Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R273P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001170535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATAD3A | NM_001170535.3 | c.817C>T | p.Arg273Cys | missense_variant | 8/16 | ENST00000378756.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATAD3A | ENST00000378756.8 | c.817C>T | p.Arg273Cys | missense_variant | 8/16 | 1 | NM_001170535.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151396Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248838Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135130
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459730Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 726250
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151512Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74054
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 26, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at