Variant chr1-154925080-GC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006556.4(PMVK):c.*48del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 1,459,192 control chromosomes in the GnomAD database, including 263 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 185 hom., cov: 26)

Exomes 𝑓: 0.0023 ( 78 hom. )

Consequence

PMVK
NM_006556.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00600

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]

PMVK links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-154925080-GC-G is Benign according to our data. Variant chr1-154925080-GC-G is described in ClinVar as [Benign]. Clinvar id is 1259917.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PMVK	NM_006556.4 linkuse as main transcript	c.*48del	3_prime_UTR_variant	5/5	ENST00000368467.4
PMVK	NM_001323011.3 linkuse as main transcript	c.*48del	3_prime_UTR_variant	5/5
PMVK	NM_001323012.3 linkuse as main transcript	c.*48del	3_prime_UTR_variant	5/5
PMVK	NM_001348696.2 linkuse as main transcript	c.*48del	3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PMVK	ENST00000368467.4 linkuse as main transcript	c.*48del		3_prime_UTR_variant	5/5	1	NM_006556.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0270

AC:

3944

AN:

145960

Hom.:

186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0920

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0121

Gnomad ASJ

AF:

0.0223

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000214

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0333

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.0212

GnomAD3 exomes

AF:

0.00870

AC:

2086

AN:

239750

Hom.:

AF XY:

0.00680

AC XY:

882

AN XY:

129766

show subpopulations

Gnomad AFR exome

AF:

0.0942

Gnomad AMR exome

AF:

0.00646

Gnomad ASJ exome

AF:

0.0200

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000137

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00152

Gnomad OTH exome

AF:

0.00724

GnomAD4 exome

AF:

0.00230

AC:

3022

AN:

1313148

Hom.:

Cov.:

AF XY:

0.00210

AC XY:

1370

AN XY:

651308

show subpopulations

Gnomad4 AFR exome

AF:

0.0618

Gnomad4 AMR exome

AF:

0.00568

Gnomad4 ASJ exome

AF:

0.0146

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000285

Gnomad4 FIN exome

AF:

0.0000223

Gnomad4 NFE exome

AF:

0.000473

Gnomad4 OTH exome

AF:

0.00443

GnomAD4 genome

AF:

0.0270

AC:

3946

AN:

146044

Hom.:

185

Cov.:

AF XY:

0.0262

AC XY:

1859

AN XY:

70834

show subpopulations

Gnomad4 AFR

AF:

0.0918

Gnomad4 AMR

AF:

0.0121

Gnomad4 ASJ

AF:

0.0223

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000214

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00109

Gnomad4 OTH

AF:

0.0210

Alfa

AF:

0.0193

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over