10-46584559-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031912.5(SYT15):c.887C>A(p.Thr296Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. T296M) has been classified as Uncertain significance.
Frequency
Consequence
NM_031912.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151892Hom.: 0 Cov.: 34
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151892Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74176
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.887C>A (p.T296K) alteration is located in exon 6 (coding exon 6) of the SYT15 gene. This alteration results from a C to A substitution at nucleotide position 887, causing the threonine (T) at amino acid position 296 to be replaced by a lysine (K). 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