chr13-25372298-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_016529.6(ATP8A2):c.76+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 1,464,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016529.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00101 AC: 154AN: 151778Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00117 AC: 105AN: 89790Hom.: 0 AF XY: 0.00117 AC XY: 59AN XY: 50576
GnomAD4 exome AF: 0.00127 AC: 1671AN: 1313054Hom.: 0 Cov.: 31 AF XY: 0.00131 AC XY: 848AN XY: 647602
GnomAD4 genome AF: 0.00101 AC: 154AN: 151778Hom.: 0 Cov.: 32 AF XY: 0.000971 AC XY: 72AN XY: 74146
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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ATP8A2-related disorder Benign:1
This variant is classified as 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