chr1-154929049-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_006556.4(PMVK):ā€‹c.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

Scores

4
15

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 5.99
Variant links:
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
PMVKNM_006556.4 linkuse as main transcriptc.287T>C p.Val96Ala missense_variant 3/5 ENST00000368467.4
PMVKNM_001323011.3 linkuse as main transcriptc.245T>C p.Val82Ala missense_variant 3/5
PMVKNM_001323012.3 linkuse as main transcriptc.62T>C p.Val21Ala missense_variant 3/5
PMVKNM_001348696.2 linkuse as main transcriptc.62T>C p.Val21Ala missense_variant 3/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PMVKENST00000368467.4 linkuse as main transcriptc.287T>C p.Val96Ala missense_variant 3/51 NM_006556.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00436
AC:
664
AN:
152170
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00118
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.00321
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00748
Gnomad OTH
AF:
0.00717
GnomAD3 exomes
AF:
0.00431
AC:
1083
AN:
251470
Hom.:
6
AF XY:
0.00433
AC XY:
589
AN XY:
135910
show subpopulations
Gnomad AFR exome
AF:
0.000923
Gnomad AMR exome
AF:
0.00147
Gnomad ASJ exome
AF:
0.000298
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00140
Gnomad FIN exome
AF:
0.00249
Gnomad NFE exome
AF:
0.00784
Gnomad OTH exome
AF:
0.00391
GnomAD4 exome
AF:
0.00612
AC:
8953
AN:
1461844
Hom.:
32
Cov.:
31
AF XY:
0.00605
AC XY:
4398
AN XY:
727224
show subpopulations
Gnomad4 AFR exome
AF:
0.000896
Gnomad4 AMR exome
AF:
0.00170
Gnomad4 ASJ exome
AF:
0.000230
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00141
Gnomad4 FIN exome
AF:
0.00296
Gnomad4 NFE exome
AF:
0.00739
Gnomad4 OTH exome
AF:
0.00558
GnomAD4 genome
AF:
0.00436
AC:
664
AN:
152288
Hom.:
2
Cov.:
32
AF XY:
0.00380
AC XY:
283
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.00118
Gnomad4 AMR
AF:
0.00320
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00188
Gnomad4 NFE
AF:
0.00747
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00640
Hom.:
8
Bravo
AF:
0.00454
TwinsUK
AF:
0.00647
AC:
24
ALSPAC
AF:
0.00493
AC:
19
ESP6500AA
AF:
0.00113
AC:
5
ESP6500EA
AF:
0.00779
AC:
67
ExAC
AF:
0.00518
AC:
629
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

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 providedclinical testingPreventionGenetics, part of Exact SciencesOct 22, 2019This 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 submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsNov 07, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.25
T
Eigen
Benign
0.083
Eigen_PC
Benign
0.15
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.70
T
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.0086
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.4
M
MutationTaster
Benign
0.98
D
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.18
Sift
Benign
0.17
T
Sift4G
Benign
0.22
T
Polyphen
0.67
P
Vest4
0.61
MVP
0.39
MPC
0.92
ClinPred
0.025
T
GERP RS
5.9
Varity_R
0.41
gMVP
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs139248801; hg19: chr1-154901525; COSMIC: COSV100870502; API