3-52706092-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000233025.11(SPCS1):c.47C>G(p.Ser16Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S16Y) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000233025.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPCS1 | ENST00000233025.11 | c.47C>G | p.Ser16Cys | missense_variant | Exon 1 of 4 | 1 | ENSP00000233025.7 | |||
SPCS1 | ENST00000423431.5 | c.-30-552C>G | intron_variant | Intron 1 of 3 | 3 | ENSP00000391610.1 | ||||
SPCS1 | ENST00000619898.5 | c.-155C>G | upstream_gene_variant | 1 | NM_014041.5 | ENSP00000478310.2 | ||||
SPCS1 | ENST00000448693.2 | n.-17C>G | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at