15-64096059-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003099.5(SNX1):c.46C>T(p.Pro16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 1,586,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003099.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX1 | NM_003099.5 | c.46C>T | p.Pro16Ser | missense_variant | Exon 1 of 15 | ENST00000559844.6 | NP_003090.2 | |
SNX1 | NM_001242933.2 | c.46C>T | p.Pro16Ser | missense_variant | Exon 1 of 15 | NP_001229862.1 | ||
SNX1 | NM_148955.4 | c.46C>T | p.Pro16Ser | missense_variant | Exon 1 of 13 | NP_683758.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000746 AC: 15AN: 201114Hom.: 1 AF XY: 0.0000825 AC XY: 9AN XY: 109070
GnomAD4 exome AF: 0.0000209 AC: 30AN: 1434456Hom.: 0 Cov.: 32 AF XY: 0.0000225 AC XY: 16AN XY: 711756
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.46C>T (p.P16S) alteration is located in exon 1 (coding exon 1) of the SNX1 gene. This alteration results from a C to T substitution at nucleotide position 46, causing the proline (P) at amino acid position 16 to be replaced by a serine (S). 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