rs768177407
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004320.6(ATP2A1):c.2455C>T(p.Arg819Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R819H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004320.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.2455C>T | p.Arg819Cys | missense_variant | 17/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.2455C>T | p.Arg819Cys | missense_variant | 17/22 | ||
ATP2A1 | NM_001286075.2 | c.2080C>T | p.Arg694Cys | missense_variant | 15/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.2455C>T | p.Arg819Cys | missense_variant | 17/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.2455C>T | p.Arg819Cys | missense_variant | 17/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.2080C>T | p.Arg694Cys | missense_variant | 15/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250690Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135760
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74292
ClinVar
Submissions by phenotype
Brody myopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 26, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 25, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at