chr1-154929049-A-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006556.4(PMVK):āc.287T>Cā(p.Val96Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00596 in 1,614,132 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0044 ( 2 hom., cov: 32)
Exomes š: 0.0061 ( 32 hom. )
Consequence
PMVK
NM_006556.4 missense
NM_006556.4 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 5.99
Genes affected
PMVK (HGNC:9141): (phosphomevalonate kinase) This gene encodes a peroxisomal enzyme that is a member of the galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase (GHMP) family of ATP-dependent enzymes. The encoded protein catalyzes the conversion of mevalonate 5-phosphate to mevalonate 5-diphosphate, which is the fifth step in the mevalonate pathway of isoprenoid biosynthesis. Mutations in this gene are linked to certain types of porokeratosis including disseminated superficial porokeratosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.008589804).
BP6
Variant 1-154929049-A-G is Benign according to our data. Variant chr1-154929049-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 377095.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 664 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMVK | NM_006556.4 | c.287T>C | p.Val96Ala | missense_variant | 3/5 | ENST00000368467.4 | |
PMVK | NM_001323011.3 | c.245T>C | p.Val82Ala | missense_variant | 3/5 | ||
PMVK | NM_001323012.3 | c.62T>C | p.Val21Ala | missense_variant | 3/5 | ||
PMVK | NM_001348696.2 | c.62T>C | p.Val21Ala | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMVK | ENST00000368467.4 | c.287T>C | p.Val96Ala | missense_variant | 3/5 | 1 | NM_006556.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00436 AC: 664AN: 152170Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00431 AC: 1083AN: 251470Hom.: 6 AF XY: 0.00433 AC XY: 589AN XY: 135910
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GnomAD4 exome AF: 0.00612 AC: 8953AN: 1461844Hom.: 32 Cov.: 31 AF XY: 0.00605 AC XY: 4398AN XY: 727224
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GnomAD4 genome AF: 0.00436 AC: 664AN: 152288Hom.: 2 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PMVK-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 07, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at