rs1803738
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170665.4(ATP2A2):c.*623T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000359 in 1,113,194 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.
Frequency
Genomes: 𝑓 0.0000071 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000031 ( 0 hom. )
Consequence
ATP2A2
NM_170665.4 3_prime_UTR
NM_170665.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.06
Genes affected
ATP2A2 (HGNC:812): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of the skeletal muscle. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol into the sarcoplasmic reticulum lumen, and is involved in regulation of the contraction/relaxation cycle. Mutations in this gene cause Darier-White disease, also known as keratosis follicularis, an autosomal dominant skin disorder characterized by loss of adhesion between epidermal cells and abnormal keratinization. Other types of mutations in this gene have been associated with various forms of muscular dystrophies. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2019]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2A2 | NM_170665.4 | c.*623T>A | 3_prime_UTR_variant | 20/20 | ENST00000539276.7 | NP_733765.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2A2 | ENST00000539276.7 | c.*623T>A | 3_prime_UTR_variant | 20/20 | 1 | NM_170665.4 | ENSP00000440045.2 |
Frequencies
GnomAD3 genomes AF: 0.00000713 AC: 1AN: 140188Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00000308 AC: 3AN: 973006Hom.: 0 Cov.: 34 AF XY: 0.00000217 AC XY: 1AN XY: 460874
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GnomAD4 genome AF: 0.00000713 AC: 1AN: 140188Hom.: 0 Cov.: 30 AF XY: 0.0000146 AC XY: 1AN XY: 68288
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at