rs2298566
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014758.3(SNX19):āc.2633T>Gā(p.Leu878Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,608,974 control chromosomes in the GnomAD database, including 461,553 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_014758.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.797 AC: 121140AN: 151990Hom.: 48886 Cov.: 32
GnomAD3 exomes AF: 0.773 AC: 193604AN: 250368Hom.: 75298 AF XY: 0.773 AC XY: 104529AN XY: 135298
GnomAD4 exome AF: 0.751 AC: 1094346AN: 1456866Hom.: 412622 Cov.: 48 AF XY: 0.753 AC XY: 545364AN XY: 723966
GnomAD4 genome AF: 0.797 AC: 121242AN: 152108Hom.: 48931 Cov.: 32 AF XY: 0.797 AC XY: 59264AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at