Variant 17-7583790-A-G 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 ENST00000655859.2(MPDU1-AS1):n.181+128T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,478,702 control chromosomes in the GnomAD database, including 24,481 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3689 hom., cov: 34)

Exomes 𝑓: 0.17 ( 20792 hom. )

Consequence

MPDU1-AS1
ENST00000655859.2 intron, non_coding_transcript

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.244

Variant links:

Genes affected

MPDU1-AS1 (HGNC:40379): (MPDU1 antisense RNA 1)

MPDU1-AS1 links:

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=-0.76).

BP6

Variant 17-7583790-A-G is Benign according to our data. Variant chr17-7583790-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 325511.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MPDU1	NM_001330073.1 linkuse as main transcript	c.-73A>G	5_prime_UTR_variant	1/6
MPDU1	XM_006721597.3 linkuse as main transcript	c.-73A>G	5_prime_UTR_variant	1/6
MPDU1	XM_006721598.4 linkuse as main transcript	c.-73A>G	5_prime_UTR_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPDU1-AS1	ENST00000655859.2 linkuse as main transcript	n.181+128T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31441

AN:

152158

Hom.:

3680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.194

AC:

48110

AN:

248430

Hom.:

5255

AF XY:

0.188

AC XY:

25345

AN XY:

134654

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.203

Gnomad ASJ exome

AF:

0.144

Gnomad EAS exome

AF:

0.353

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.167

AC:

222155

AN:

1326426

Hom.:

20792

Cov.:

AF XY:

0.168

AC XY:

111690

AN XY:

666726

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.394

Gnomad4 SAS exome

AF:

0.201

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.207

AC:

31479

AN:

152276

Hom.:

3689

Cov.:

AF XY:

0.210

AC XY:

15657

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.144

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.198

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.159

Hom.:

2216

Bravo

AF:

0.211

Asia WGS

AF:

0.277

AC:

961

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

2.0

DANN

Benign

0.75

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