16-28884632-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004320.6(ATP2A1):c.521G>T(p.Arg174Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004320.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.521G>T | p.Arg174Leu | missense_variant | Exon 6 of 23 | ENST00000395503.9 | NP_004311.1 | |
ATP2A1 | NM_173201.5 | c.521G>T | p.Arg174Leu | missense_variant | Exon 6 of 22 | NP_775293.1 | ||
ATP2A1 | NM_001286075.2 | c.146G>T | p.Arg49Leu | missense_variant | Exon 4 of 21 | NP_001273004.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.521G>T | p.Arg174Leu | missense_variant | Exon 6 of 23 | 1 | NM_004320.6 | ENSP00000378879.5 | ||
ATP2A1 | ENST00000357084.7 | c.521G>T | p.Arg174Leu | missense_variant | Exon 6 of 22 | 2 | ENSP00000349595.3 | |||
ATP2A1 | ENST00000536376.5 | c.146G>T | p.Arg49Leu | missense_variant | Exon 4 of 21 | 2 | ENSP00000443101.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250676Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135626
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461436Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727048
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at