16-28894763-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004320.6(ATP2A1):c.1288-59G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 1,607,682 control chromosomes in the GnomAD database, including 359,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004320.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.1288-59G>C | intron_variant | Intron 11 of 22 | ENST00000395503.9 | NP_004311.1 | ||
ATP2A1 | NM_173201.5 | c.1288-59G>C | intron_variant | Intron 11 of 21 | NP_775293.1 | |||
ATP2A1 | NM_001286075.2 | c.913-59G>C | intron_variant | Intron 9 of 20 | NP_001273004.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1288-59G>C | intron_variant | Intron 11 of 22 | 1 | NM_004320.6 | ENSP00000378879.5 | |||
ATP2A1 | ENST00000357084.7 | c.1288-59G>C | intron_variant | Intron 11 of 21 | 2 | ENSP00000349595.3 | ||||
ATP2A1 | ENST00000536376.5 | c.913-59G>C | intron_variant | Intron 9 of 20 | 2 | ENSP00000443101.1 | ||||
ATP2A1 | ENST00000564732.1 | n.315-59G>C | intron_variant | Intron 3 of 6 | 5 | ENSP00000457357.1 |
Frequencies
GnomAD3 genomes AF: 0.685 AC: 103899AN: 151668Hom.: 36105 Cov.: 29
GnomAD4 exome AF: 0.663 AC: 965323AN: 1455896Hom.: 323468 Cov.: 43 AF XY: 0.667 AC XY: 483499AN XY: 724402
GnomAD4 genome AF: 0.685 AC: 103925AN: 151786Hom.: 36099 Cov.: 29 AF XY: 0.685 AC XY: 50785AN XY: 74172
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at