chr9-127936362-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003863.4(DPM2):c.196+191C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,535,314 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 11 hom., cov: 33)
Exomes 𝑓: 0.00092 ( 3 hom. )
Consequence
DPM2
NM_003863.4 intron
NM_003863.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.352
Genes affected
DPM2 (HGNC:3006): (dolichyl-phosphate mannosyltransferase subunit 2, regulatory) Dolichol-phosphate mannose (Dol-P-Man) serves as a donor of mannosyl residues on the lumenal side of the endoplasmic reticulum (ER). Lack of Dol-P-Man results in defective surface expression of GPI-anchored proteins. Dol-P-Man is synthesized from GDP-mannose and dolichol-phosphate on the cytosolic side of the ER by the enzyme dolichyl-phosphate mannosyltransferase. The protein encoded by this gene is a hydrophobic protein that contains 2 predicted transmembrane domains and a putative ER localization signal near the C terminus. This protein associates with DPM1 in vivo and is required for the ER localization and stable expression of DPM1 and also enhances the binding of dolichol-phosphate to DPM1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-127936362-G-C is Benign according to our data. Variant chr9-127936362-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1196032.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00692 (1053/152222) while in subpopulation AFR AF= 0.0231 (958/41524). AF 95% confidence interval is 0.0219. There are 11 homozygotes in gnomad4. There are 487 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPM2 | NM_003863.4 | c.196+191C>G | intron_variant | ENST00000314392.13 | |||
DPM2 | NM_001378437.1 | c.106+191C>G | intron_variant | ||||
DPM2 | NR_165631.1 | n.353+191C>G | intron_variant, non_coding_transcript_variant | ||||
DPM2 | NR_165632.1 | n.38-582C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPM2 | ENST00000314392.13 | c.196+191C>G | intron_variant | 1 | NM_003863.4 | P1 | |||
ENST00000592240.5 | n.143+1717G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00690 AC: 1050AN: 152104Hom.: 11 Cov.: 33
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GnomAD3 exomes AF: 0.00197 AC: 277AN: 140476Hom.: 2 AF XY: 0.00148 AC XY: 111AN XY: 74994
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GnomAD4 exome AF: 0.000919 AC: 1271AN: 1383092Hom.: 3 Cov.: 30 AF XY: 0.000810 AC XY: 551AN XY: 680574
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GnomAD4 genome AF: 0.00692 AC: 1053AN: 152222Hom.: 11 Cov.: 33 AF XY: 0.00654 AC XY: 487AN XY: 74430
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at