Variant 17-7587061-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004870.4(MPDU1):c.507+44G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,451,628 control chromosomes in the GnomAD database, including 238,653 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17527 hom., cov: 20)

Exomes 𝑓: 0.57 ( 221126 hom. )

Consequence

MPDU1
NM_004870.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.706

Variant links:

Genes affected

MPDU1 (HGNC:7207): (mannose-P-dolichol utilization defect 1) This gene encodes an endoplasmic reticulum membrane protein that is required for utilization of the mannose donor mannose-P-dolichol in the synthesis of lipid-linked oligosaccharides and glycosylphosphatidylinositols. Mutations in this gene result in congenital disorder of glycosylation type If. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

MPDU1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-7587061-G-C is Benign according to our data. Variant chr17-7587061-G-C is described in ClinVar as [Benign]. Clinvar id is 259559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPDU1	NM_004870.4 linkuse as main transcript	c.507+44G>C		intron_variant		ENST00000250124.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPDU1	ENST00000250124.11 linkuse as main transcript	c.507+44G>C		intron_variant		1	NM_004870.4	P1	O75352-1

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

68099

AN:

145146

Hom.:

17528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.651

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.635

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.490

GnomAD3 exomes

AF:

0.524

AC:

127702

AN:

243620

Hom.:

34891

AF XY:

0.542

AC XY:

71896

AN XY:

132680

show subpopulations

Gnomad AFR exome

AF:

0.287

Gnomad AMR exome

AF:

0.360

Gnomad ASJ exome

AF:

0.657

Gnomad EAS exome

AF:

0.437

Gnomad SAS exome

AF:

0.635

Gnomad FIN exome

AF:

0.488

Gnomad NFE exome

AF:

0.584

Gnomad OTH exome

AF:

0.561

GnomAD4 exome

AF:

0.572

AC:

746688

AN:

1306362

Hom.:

221126

Cov.:

AF XY:

0.575

AC XY:

377120

AN XY:

656134

show subpopulations

Gnomad4 AFR exome

AF:

0.281

Gnomad4 AMR exome

AF:

0.372

Gnomad4 ASJ exome

AF:

0.659

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.639

Gnomad4 FIN exome

AF:

0.486

Gnomad4 NFE exome

AF:

0.592

Gnomad4 OTH exome

AF:

0.567

GnomAD4 genome

AF:

0.469

AC:

68122

AN:

145266

Hom.:

17527

Cov.:

AF XY:

0.467

AC XY:

32867

AN XY:

70414

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.651

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.635

Gnomad4 FIN

AF:

0.479

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.453

Hom.:

2148

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.20

DANN

Benign

0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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