Variant chr1-154928774-A-AAAAT 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.312+249_312+250insATTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 7675 hom., cov: 0)

Consequence

PMVK
NM_006556.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.584

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 1-154928774-A-AAAAT is Benign according to our data. Variant chr1-154928774-A-AAAAT is described in ClinVar as [Benign]. Clinvar id is 1257436.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PMVK	NM_006556.4 linkuse as main transcript	c.312+249_312+250insATTT	intron_variant	ENST00000368467.4
PMVK	NM_001323011.3 linkuse as main transcript	c.270+249_270+250insATTT	intron_variant
PMVK	NM_001323012.3 linkuse as main transcript	c.87+249_87+250insATTT	intron_variant
PMVK	NM_001348696.2 linkuse as main transcript	c.87+249_87+250insATTT	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PMVK	ENST00000368467.4 linkuse as main transcript	c.312+249_312+250insATTT		intron_variant		1	NM_006556.4	P1

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

45884

AN:

141762

Hom.:

7669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.301

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.324

AC:

45914

AN:

141816

Hom.:

7675

Cov.:

AF XY:

0.325

AC XY:

22273

AN XY:

68544

show subpopulations

Gnomad4 AFR

AF:

0.372

Gnomad4 AMR

AF:

0.254

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.297

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.341

Gnomad4 NFE

AF:

0.324

Gnomad4 OTH

AF:

0.306

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 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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