3-52706151-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000233025.11(SPCS1):c.106C>T(p.Gln36*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,612 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000233025.11 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPCS1 | ENST00000619898 | c.-96C>T | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_014041.5 | ENSP00000478310.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390612Hom.: 0 Cov.: 30 AF XY: 0.00000146 AC XY: 1AN XY: 686620
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at