11-130880691-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014758.3(SNX19):c.2689G>A(p.Val897Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000422 in 1,612,530 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014758.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250662Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135440
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1460248Hom.: 1 Cov.: 30 AF XY: 0.0000496 AC XY: 36AN XY: 726206
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2689G>A (p.V897I) alteration is located in exon 9 (coding exon 9) of the SNX19 gene. This alteration results from a G to A substitution at nucleotide position 2689, causing the valine (V) at amino acid position 897 to be replaced by an isoleucine (I). 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