16-28894527-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004320.6(ATP2A1):āc.1207C>Gā(p.Arg403Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R403W) has been classified as Likely benign.
Frequency
Consequence
NM_004320.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.1207C>G | p.Arg403Gly | missense_variant | 11/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.1207C>G | p.Arg403Gly | missense_variant | 11/22 | ||
ATP2A1 | NM_001286075.2 | c.832C>G | p.Arg278Gly | missense_variant | 9/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1207C>G | p.Arg403Gly | missense_variant | 11/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.1207C>G | p.Arg403Gly | missense_variant | 11/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.832C>G | p.Arg278Gly | missense_variant | 9/21 | 2 | |||
ATP2A1 | ENST00000564732.1 | c.316+284C>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727198
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at