rs74336587
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004870.4(MPDU1):c.302+21C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 1,612,516 control chromosomes in the GnomAD database, including 595 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 44 hom., cov: 31)
Exomes 𝑓: 0.026 ( 551 hom. )
Consequence
MPDU1
NM_004870.4 intron
NM_004870.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.162
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]
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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=-0.81).
BP6
?
Variant 17-7586099-C-T is Benign according to our data. Variant chr17-7586099-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 259558.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0185 (2810/152262) while in subpopulation NFE AF= 0.0277 (1886/68010). AF 95% confidence interval is 0.0267. There are 44 homozygotes in gnomad4. There are 1339 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 44 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPDU1 | NM_004870.4 | c.302+21C>T | intron_variant | ENST00000250124.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPDU1 | ENST00000250124.11 | c.302+21C>T | intron_variant | 1 | NM_004870.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0185 AC: 2809AN: 152144Hom.: 44 Cov.: 31
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GnomAD3 exomes AF: 0.0223 AC: 5587AN: 250732Hom.: 76 AF XY: 0.0228 AC XY: 3087AN XY: 135538
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GnomAD4 exome AF: 0.0257 AC: 37540AN: 1460254Hom.: 551 Cov.: 32 AF XY: 0.0259 AC XY: 18833AN XY: 726452
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GnomAD4 genome ? AF: 0.0185 AC: 2810AN: 152262Hom.: 44 Cov.: 31 AF XY: 0.0180 AC XY: 1339AN XY: 74452
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 17, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at