rs4149796
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004203.5(PKMYT1):c.418C>T(p.Arg140Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,599,524 control chromosomes in the GnomAD database, including 1 homozygotes. 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R140H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004203.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKMYT1 | NM_004203.5 | c.418C>T | p.Arg140Cys | missense_variant | 4/9 | ENST00000262300.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKMYT1 | ENST00000262300.13 | c.418C>T | p.Arg140Cys | missense_variant | 4/9 | 1 | NM_004203.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000269 AC: 41AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000436 AC: 102AN: 234016Hom.: 1 AF XY: 0.000388 AC XY: 50AN XY: 128920
GnomAD4 exome AF: 0.000148 AC: 214AN: 1447152Hom.: 1 Cov.: 31 AF XY: 0.000130 AC XY: 94AN XY: 720418
GnomAD4 genome ? AF: 0.000269 AC: 41AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74506
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at