chr10-46580926-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_031912.5(SYT15):āc.245C>Gā(p.Thr82Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000712 in 140,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT15 | NM_031912.5 | c.245C>G | p.Thr82Ser | missense_variant | 3/8 | ENST00000374321.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT15 | ENST00000374321.9 | c.245C>G | p.Thr82Ser | missense_variant | 3/8 | 2 | NM_031912.5 | P1 | |
SYT15-AS1 | ENST00000659936.1 | n.2530G>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.00000712 AC: 1AN: 140544Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248356Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134710
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000384 AC: 46AN: 1199084Hom.: 0 Cov.: 20 AF XY: 0.0000373 AC XY: 22AN XY: 589178
GnomAD4 genome AF: 0.00000712 AC: 1AN: 140544Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 68338
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at