12-110342302-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_170665.4(ATP2A2):c.2172G>T(p.Ala724=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. A724A) has been classified as Benign.
Frequency
Consequence
NM_170665.4 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 |
---|---|---|---|---|---|---|---|
ATP2A2 | NM_170665.4 | c.2172G>T | p.Ala724= | synonymous_variant | 15/20 | ENST00000539276.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A2 | ENST00000539276.7 | c.2172G>T | p.Ala724= | synonymous_variant | 15/20 | 1 | NM_170665.4 | P3 | |
ATP2A2 | ENST00000308664.10 | c.2172G>T | p.Ala724= | synonymous_variant | 15/21 | 1 | A1 | ||
ATP2A2 | ENST00000548169.2 | c.1845G>T | p.Ala615= | synonymous_variant | 11/16 | 2 | |||
ATP2A2 | ENST00000377685.9 | c.*2012G>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/20 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at