10-132224463-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173575.4(STK32C):c.937G>A(p.Val313Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000922 in 1,572,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173575.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK32C | NM_173575.4 | c.937G>A | p.Val313Met | missense_variant | Exon 8 of 12 | ENST00000298630.8 | NP_775846.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK32C | ENST00000298630.8 | c.937G>A | p.Val313Met | missense_variant | Exon 8 of 12 | 1 | NM_173575.4 | ENSP00000298630.3 | ||
STK32C | ENST00000368622.5 | c.586G>A | p.Val196Met | missense_variant | Exon 8 of 12 | 1 | ENSP00000357611.1 | |||
STK32C | ENST00000462160.5 | n.754G>A | non_coding_transcript_exon_variant | Exon 8 of 13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000145 AC: 27AN: 186426Hom.: 0 AF XY: 0.000182 AC XY: 18AN XY: 99166
GnomAD4 exome AF: 0.0000958 AC: 136AN: 1420178Hom.: 0 Cov.: 31 AF XY: 0.000101 AC XY: 71AN XY: 702258
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.937G>A (p.V313M) alteration is located in exon 8 (coding exon 8) of the STK32C gene. This alteration results from a G to A substitution at nucleotide position 937, causing the valine (V) at amino acid position 313 to be replaced by a methionine (M). 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