18-79096499-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198531.5(ATP9B):c.143C>T(p.Ala48Val) variant causes a missense change. The variant allele was found at a frequency of 0.000341 in 1,613,830 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198531.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000291 AC: 73AN: 251184Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135750
GnomAD4 exome AF: 0.000361 AC: 528AN: 1461658Hom.: 1 Cov.: 31 AF XY: 0.000421 AC XY: 306AN XY: 727142
GnomAD4 genome AF: 0.000151 AC: 23AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.143C>T (p.A48V) alteration is located in exon 2 (coding exon 2) of the ATP9B gene. This alteration results from a C to T substitution at nucleotide position 143, causing the alanine (A) at amino acid position 48 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at