17-3928753-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005173.4(ATP2A3):c.2890G>A(p.Gly964Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,553,218 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005173.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151972Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000251 AC: 4AN: 159354Hom.: 0 AF XY: 0.0000119 AC XY: 1AN XY: 84268
GnomAD4 exome AF: 0.0000443 AC: 62AN: 1401128Hom.: 0 Cov.: 32 AF XY: 0.0000419 AC XY: 29AN XY: 691340
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2890G>A (p.G964R) alteration is located in exon 20 (coding exon 20) of the ATP2A3 gene. This alteration results from a G to A substitution at nucleotide position 2890, causing the glycine (G) at amino acid position 964 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at