2-27374351-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_014748.4(SNX17):c.529C>T(p.Arg177Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000074 in 1,607,930 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R177Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_014748.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX17 | NM_014748.4 | c.529C>T | p.Arg177Trp | missense_variant | 7/15 | ENST00000233575.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX17 | ENST00000233575.7 | c.529C>T | p.Arg177Trp | missense_variant | 7/15 | 1 | NM_014748.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000268 AC: 4AN: 149514Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250798Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135800
GnomAD4 exome AF: 0.0000789 AC: 115AN: 1458416Hom.: 0 Cov.: 34 AF XY: 0.0000841 AC XY: 61AN XY: 725706
GnomAD4 genome ? AF: 0.0000268 AC: 4AN: 149514Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72666
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.529C>T (p.R177W) alteration is located in exon 7 (coding exon 7) of the SNX17 gene. This alteration results from a C to T substitution at nucleotide position 529, causing the arginine (R) at amino acid position 177 to be replaced by a tryptophan (W). 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