10-46580995-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_031912.5(SYT15):c.314C>T(p.Pro105Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/12 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 18AN: 134432Hom.: 4 Cov.: 22 FAILED QC
GnomAD3 exomes AF: 0.0000524 AC: 13AN: 248190Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134780
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000439 AC: 45AN: 1025138Hom.: 4 Cov.: 14 AF XY: 0.0000296 AC XY: 15AN XY: 506910
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000134 AC: 18AN: 134530Hom.: 4 Cov.: 22 AF XY: 0.000107 AC XY: 7AN XY: 65240
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.314C>T (p.P105L) alteration is located in exon 3 (coding exon 3) of the SYT15 gene. This alteration results from a C to T substitution at nucleotide position 314, causing the proline (P) at amino acid position 105 to be replaced by a leucine (L). 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