chr17-3925408-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_174955.3(ATP2A3):āc.3102A>Gā(p.Arg1034Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,613,220 control chromosomes in the GnomAD database, including 104,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_174955.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.322 AC: 48944AN: 151776Hom.: 8333 Cov.: 31
GnomAD3 exomes AF: 0.352 AC: 87833AN: 249482Hom.: 16034 AF XY: 0.350 AC XY: 47234AN XY: 134974
GnomAD4 exome AF: 0.360 AC: 526316AN: 1461326Hom.: 95894 Cov.: 50 AF XY: 0.358 AC XY: 260513AN XY: 726950
GnomAD4 genome AF: 0.323 AC: 49005AN: 151894Hom.: 8348 Cov.: 31 AF XY: 0.321 AC XY: 23842AN XY: 74234
ClinVar
Submissions by phenotype
ATP2A3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at