chr17-3925403-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000572116.1(ATP2A3):āc.404A>Gā(p.Glu135Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000631 in 1,613,864 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
ENST00000572116.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A3 | NM_005173.4 | c.*19A>G | 3_prime_UTR_variant | 21/21 | ENST00000397041.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A3 | ENST00000397041.8 | c.*19A>G | 3_prime_UTR_variant | 21/21 | 1 | NM_005173.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00323 AC: 491AN: 152060Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.000923 AC: 231AN: 250194Hom.: 2 AF XY: 0.000606 AC XY: 82AN XY: 135348
GnomAD4 exome AF: 0.000361 AC: 527AN: 1461686Hom.: 4 Cov.: 30 AF XY: 0.000289 AC XY: 210AN XY: 727150
GnomAD4 genome AF: 0.00323 AC: 491AN: 152178Hom.: 6 Cov.: 32 AF XY: 0.00309 AC XY: 230AN XY: 74402
ClinVar
Submissions by phenotype
ATP2A3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | 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