11-130880687-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_014758.3(SNX19):c.2693G>T(p.Arg898Met) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,612,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250716Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135484
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460390Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726314
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2693G>T (p.R898M) alteration is located in exon 9 (coding exon 9) of the SNX19 gene. This alteration results from a G to T substitution at nucleotide position 2693, causing the arginine (R) at amino acid position 898 to be replaced by a methionine (M). 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