9-35062975-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007126.5(VCP):c.811+3G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
VCP
NM_007126.5 splice_donor_region, intron
NM_007126.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.7508
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.543
Genes affected
VCP (HGNC:12666): (valosin containing protein) This gene encodes a member of the AAA ATPase family of proteins. The encoded protein plays a role in protein degradation, intracellular membrane fusion, DNA repair and replication, regulation of the cell cycle, and activation of the NF-kappa B pathway. This protein forms a homohexameric complex that interacts with a variety of cofactors and extracts ubiquitinated proteins from lipid membranes or protein complexes. Mutations in this gene cause IBMPFD (inclusion body myopathy with paget disease of bone and frontotemporal dementia), ALS (amyotrophic lateral sclerosis) and Charcot-Marie-Tooth disease in human patients. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCP | NM_007126.5 | c.811+3G>T | splice_donor_region_variant, intron_variant | ENST00000358901.11 | |||
VCP | NM_001354927.2 | c.676+3G>T | splice_donor_region_variant, intron_variant | ||||
VCP | NM_001354928.2 | c.676+3G>T | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCP | ENST00000358901.11 | c.811+3G>T | splice_donor_region_variant, intron_variant | 1 | NM_007126.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151738Hom.: 0 Cov.: 30 FAILED QC
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GnomAD4 exome Cov.: 43
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43
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151738Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74090
GnomAD4 genome
Data not reliable, filtered out with message: AC0
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at