rs140547832
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004320.6(ATP2A1):c.1851C>A(p.Ala617=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,609,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A617A) has been classified as Likely benign.
Frequency
Consequence
NM_004320.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.1851C>A | p.Ala617= | synonymous_variant | 15/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.1851C>A | p.Ala617= | synonymous_variant | 15/22 | ||
ATP2A1 | NM_001286075.2 | c.1476C>A | p.Ala492= | synonymous_variant | 13/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1851C>A | p.Ala617= | synonymous_variant | 15/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.1851C>A | p.Ala617= | synonymous_variant | 15/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.1476C>A | p.Ala492= | synonymous_variant | 13/21 | 2 | |||
ATP2A1 | ENST00000564732.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249142Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134748
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457810Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 724292
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at