3-52706092-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000233025.11(SPCS1):c.47C>A(p.Ser16Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000332 in 1,537,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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>A | p.Ser16Tyr | missense_variant | Exon 1 of 4 | 1 | ENSP00000233025.7 | |||
SPCS1 | ENST00000423431.5 | c.-30-552C>A | intron_variant | Intron 1 of 3 | 3 | ENSP00000391610.1 | ||||
SPCS1 | ENST00000619898.5 | c.-155C>A | upstream_gene_variant | 1 | NM_014041.5 | ENSP00000478310.2 | ||||
SPCS1 | ENST00000448693.2 | n.-17C>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000223 AC: 3AN: 134824Hom.: 0 AF XY: 0.0000135 AC XY: 1AN XY: 73818
GnomAD4 exome AF: 0.0000361 AC: 50AN: 1385072Hom.: 0 Cov.: 30 AF XY: 0.0000336 AC XY: 23AN XY: 683564
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.47C>A (p.S16Y) alteration is located in exon 1 (coding exon 1) of the SPCS1 gene. This alteration results from a C to A substitution at nucleotide position 47, causing the serine (S) at amino acid position 16 to be replaced by a tyrosine (Y). 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