16-84405214-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_014861.4(ATP2C2):c.297C>T(p.Ser99=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,920 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 1 hom. )
Consequence
ATP2C2
NM_014861.4 synonymous
NM_014861.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.43
Genes affected
ATP2C2 (HGNC:29103): (ATPase secretory pathway Ca2+ transporting 2) Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; cellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 16-84405214-C-T is Benign according to our data. Variant chr16-84405214-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3057295.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-5.43 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2C2 | NM_014861.4 | c.297C>T | p.Ser99= | synonymous_variant | 3/27 | ENST00000262429.9 | |
ATP2C2 | NM_001286527.3 | c.297C>T | p.Ser99= | synonymous_variant | 3/28 | ||
ATP2C2 | XM_011523486.3 | c.228C>T | p.Ser76= | synonymous_variant | 3/28 | ||
ATP2C2 | XM_047434994.1 | c.228C>T | p.Ser76= | synonymous_variant | 3/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2C2 | ENST00000262429.9 | c.297C>T | p.Ser99= | synonymous_variant | 3/27 | 1 | NM_014861.4 | P1 | |
ATP2C2 | ENST00000416219.6 | c.297C>T | p.Ser99= | synonymous_variant | 3/28 | 1 | |||
ATP2C2 | ENST00000565631.5 | n.788C>T | non_coding_transcript_exon_variant | 1/25 | 2 | ||||
ATP2C2 | ENST00000569207.5 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152062Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249174Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135176
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461740Hom.: 1 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727170
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ATP2C2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 20, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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