17-7585536-CCA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004870.4(MPDU1):c.104-195_104-194del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.47 (17236 hom., cov: 0)
• Consequence: MPDU1 NM_004870.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.675

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-7585536-CCA-C is Benign according to our data. Variant chr17-7585536-CCA-C is described in ClinVar as [Benign]. Clinvar id is 1228784.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPDU1	NM_004870.4	c.104-195_104-194del		intron_variant		ENST00000250124.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPDU1	ENST00000250124.11	c.104-195_104-194del		intron_variant		1	NM_004870.4	P1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 69306 AN: 147918 Hom.: 17243 Cov.: 0

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.468 AC: 69313 AN: 147998 Hom.: 17236 Cov.: 0 AF XY: 0.466 AC XY: 33519 AN XY: 71858

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.489

Alfa AF: 0.434 Hom.: 807

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs138315817; hg19: chr17-7488854;