rs2298566
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000265909.9(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 same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000265909.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX19 | NM_014758.3 | c.2633T>G | p.Leu878Arg | missense_variant | 9/11 | ENST00000265909.9 | NP_055573.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNX19 | ENST00000265909.9 | c.2633T>G | p.Leu878Arg | missense_variant | 9/11 | 1 | NM_014758.3 | ENSP00000265909 | P1 |
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