chr20-17952621-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014426.4(SNX5):c.479G>A(p.Arg160His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000429 in 1,613,722 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX5 | NM_014426.4 | c.479G>A | p.Arg160His | missense_variant | 5/13 | ENST00000377759.9 | |
SNX5 | NM_152227.3 | c.479G>A | p.Arg160His | missense_variant | 6/14 | ||
SNX5 | NM_001282454.2 | c.164G>A | p.Arg55His | missense_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX5 | ENST00000377759.9 | c.479G>A | p.Arg160His | missense_variant | 5/13 | 1 | NM_014426.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000339 AC: 85AN: 251048Hom.: 1 AF XY: 0.000339 AC XY: 46AN XY: 135718
GnomAD4 exome AF: 0.000443 AC: 647AN: 1461488Hom.: 2 Cov.: 30 AF XY: 0.000446 AC XY: 324AN XY: 727054
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.479G>A (p.R160H) alteration is located in exon 6 (coding exon 5) of the SNX5 gene. This alteration results from a G to A substitution at nucleotide position 479, causing the arginine (R) at amino acid position 160 to be replaced by a histidine (H). 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