chr1-154926360-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_006556.4(PMVK):c.436A>T(p.Thr146Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,920 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T146M) has been classified as Uncertain significance.
Frequency
Consequence
NM_006556.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMVK | NM_006556.4 | c.436A>T | p.Thr146Ser | missense_variant | 4/5 | ENST00000368467.4 | |
PMVK | NM_001323011.3 | c.394A>T | p.Thr132Ser | missense_variant | 4/5 | ||
PMVK | NM_001323012.3 | c.211A>T | p.Thr71Ser | missense_variant | 4/5 | ||
PMVK | NM_001348696.2 | c.211A>T | p.Thr71Ser | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMVK | ENST00000368467.4 | c.436A>T | p.Thr146Ser | missense_variant | 4/5 | 1 | NM_006556.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250220Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135318
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460758Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726688
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | PMVK: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at