10-46580325-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_031912.5(SYT15):c.169C>T(p.Arg57Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031912.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT15 | ENST00000374321.9 | c.169C>T | p.Arg57Trp | missense_variant | Exon 2 of 8 | 2 | NM_031912.5 | ENSP00000363441.4 | ||
SYT15 | ENST00000503753.5 | c.169C>T | p.Arg57Trp | missense_variant | Exon 2 of 9 | 1 | ENSP00000427607.1 | |||
SYT15 | ENST00000374323.8 | c.372-569C>T | intron_variant | Intron 1 of 6 | 2 | ENSP00000363443.3 | ||||
SYT15 | ENST00000512997.5 | c.7+1150C>T | intron_variant | Intron 1 of 2 | 2 | ENSP00000424803.1 |
Frequencies
GnomAD3 genomes AF: 0.00000981 AC: 1AN: 101934Hom.: 0 Cov.: 13
GnomAD3 exomes AF: 0.0000805 AC: 20AN: 248584Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 135030
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000910 AC: 5AN: 549184Hom.: 0 Cov.: 7 AF XY: 0.00000358 AC XY: 1AN XY: 279482
GnomAD4 genome AF: 0.00000981 AC: 1AN: 101934Hom.: 0 Cov.: 13 AF XY: 0.0000207 AC XY: 1AN XY: 48376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.169C>T (p.R57W) alteration is located in exon 2 (coding exon 2) of the SYT15 gene. This alteration results from a C to T substitution at nucleotide position 169, causing the arginine (R) at amino acid position 57 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