16-28898301-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004320.6(ATP2A1):c.1614G>T(p.Thr538=) 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. T538T) has been classified as 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.1614G>T | p.Thr538= | synonymous_variant | 14/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.1614G>T | p.Thr538= | synonymous_variant | 14/22 | ||
ATP2A1 | NM_001286075.2 | c.1239G>T | p.Thr413= | synonymous_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1614G>T | p.Thr538= | synonymous_variant | 14/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.1614G>T | p.Thr538= | synonymous_variant | 14/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.1239G>T | p.Thr413= | synonymous_variant | 12/21 | 2 | |||
ATP2A1 | ENST00000564732.1 | c.*257G>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 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