chr12-10629516-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018423.3(STYK1):āc.610A>Gā(p.Ser204Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 1,613,678 control chromosomes in the GnomAD database, including 299,771 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018423.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STYK1 | NM_018423.3 | c.610A>G | p.Ser204Gly | missense_variant | 6/11 | ENST00000075503.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STYK1 | ENST00000075503.8 | c.610A>G | p.Ser204Gly | missense_variant | 6/11 | 1 | NM_018423.3 | P1 | |
STYK1 | ENST00000542924.1 | c.124A>G | p.Ser42Gly | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.558 AC: 84785AN: 151922Hom.: 24888 Cov.: 32
GnomAD3 exomes AF: 0.634 AC: 159143AN: 250884Hom.: 51898 AF XY: 0.632 AC XY: 85737AN XY: 135608
GnomAD4 exome AF: 0.610 AC: 891551AN: 1461638Hom.: 274871 Cov.: 67 AF XY: 0.610 AC XY: 443606AN XY: 727108
GnomAD4 genome AF: 0.558 AC: 84825AN: 152040Hom.: 24900 Cov.: 32 AF XY: 0.572 AC XY: 42516AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at