rs4782970
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PVS1_ModeratePP3BP6_Very_StrongBS2
The NM_014861.4(ATP2C2):c.2482-2A>C variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00838 in 1,613,792 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014861.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00765 AC: 1165AN: 152194Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00874 AC: 2181AN: 249480Hom.: 20 AF XY: 0.00912 AC XY: 1234AN XY: 135344
GnomAD4 exome AF: 0.00846 AC: 12361AN: 1461480Hom.: 98 Cov.: 33 AF XY: 0.00845 AC XY: 6147AN XY: 727086
GnomAD4 genome AF: 0.00764 AC: 1164AN: 152312Hom.: 12 Cov.: 33 AF XY: 0.00838 AC XY: 624AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:3
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ATP2C2: BS1, BS2; ATP2C2-AS1: BS1, BS2 -
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ATP2C2-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at