3-130996904-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378687.1(ATP2C1):c.2243+108A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 813,968 control chromosomes in the GnomAD database, including 9,634 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1416 hom., cov: 33)
Exomes 𝑓: 0.15 ( 8218 hom. )
Consequence
ATP2C1
NM_001378687.1 intron
NM_001378687.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-130996904-A-C is Benign according to our data. Variant chr3-130996904-A-C is described in ClinVar as [Benign]. Clinvar id is 1265320.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2C1 | NM_001378687.1 | c.2243+108A>C | intron_variant | ENST00000510168.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2C1 | ENST00000510168.6 | c.2243+108A>C | intron_variant | 5 | NM_001378687.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.121 AC: 18368AN: 152080Hom.: 1417 Cov.: 33
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GnomAD4 exome AF: 0.148 AC: 98167AN: 661770Hom.: 8218 AF XY: 0.146 AC XY: 52202AN XY: 357402
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GnomAD4 genome AF: 0.121 AC: 18366AN: 152198Hom.: 1416 Cov.: 33 AF XY: 0.121 AC XY: 9017AN XY: 74392
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at