chr13-25469045-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP5BS1_SupportingBS2
The NM_016529.6(ATP8A2):c.145G>T(p.Asp49Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,614,058 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016529.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249346Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135368
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461740Hom.: 2 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727178
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74490
ClinVar
Submissions by phenotype
not provided Pathogenic:1
The D49Y variant in the ATP8A2 gene has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. The D49Y variant was not observed in approximately 6,200 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The D49Y variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. The D49Y variant is a good candidate for a disease-causing variant however the possibility it may be a rare benign variant cannot be excluded. -
not specified Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at