1-154926423-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006556.4(PMVK):c.373G>A(p.Val125Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,613,752 control chromosomes in the GnomAD database, including 1,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006556.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMVK | NM_006556.4 | c.373G>A | p.Val125Met | missense_variant | 4/5 | ENST00000368467.4 | |
PMVK | NM_001323011.3 | c.331G>A | p.Val111Met | missense_variant | 4/5 | ||
PMVK | NM_001323012.3 | c.148G>A | p.Val50Met | missense_variant | 4/5 | ||
PMVK | NM_001348696.2 | c.148G>A | p.Val50Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMVK | ENST00000368467.4 | c.373G>A | p.Val125Met | missense_variant | 4/5 | 1 | NM_006556.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0594 AC: 9032AN: 152150Hom.: 890 Cov.: 32
GnomAD3 exomes AF: 0.0170 AC: 4261AN: 250886Hom.: 363 AF XY: 0.0128 AC XY: 1735AN XY: 135692
GnomAD4 exome AF: 0.00712 AC: 10407AN: 1461484Hom.: 806 Cov.: 31 AF XY: 0.00628 AC XY: 4563AN XY: 727072
GnomAD4 genome AF: 0.0594 AC: 9052AN: 152268Hom.: 891 Cov.: 32 AF XY: 0.0571 AC XY: 4254AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at