rs61731516
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001378687.1(ATP2C1):c.1623G>A(p.Leu541=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000124 in 1,613,420 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
ATP2C1
NM_001378687.1 synonymous
NM_001378687.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.99
Genes affected
ATP2C1 (HGNC:13211): (ATPase secretory pathway Ca2+ transporting 1) The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium ions. Defects in this gene cause Hailey-Hailey disease, an autosomal dominant disorder. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2C1 | NM_001378687.1 | c.1623G>A | p.Leu541= | synonymous_variant | 19/28 | ENST00000510168.6 | NP_001365616.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2C1 | ENST00000510168.6 | c.1623G>A | p.Leu541= | synonymous_variant | 19/28 | 5 | NM_001378687.1 | ENSP00000427461 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151980Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461440Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727022
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151980Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74240
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ClinVar
Not reported inComputational scores
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Benign
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DANN
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RBP_binding_hub_radar
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at