NM_007126.5:c.*1035delA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_007126.5(VCP):c.*1035delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 144,440 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0027 ( 4 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
VCP
NM_007126.5 3_prime_UTR
NM_007126.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.839
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 Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00271 (391/144440) while in subpopulation SAS AF= 0.0254 (116/4560). AF 95% confidence interval is 0.0217. There are 4 homozygotes in gnomad4. There are 231 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 391 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCP | NM_007126.5 | c.*1035delA | 3_prime_UTR_variant | Exon 17 of 17 | ENST00000358901.11 | NP_009057.1 | ||
VCP | NM_001354927.2 | c.*1035delA | 3_prime_UTR_variant | Exon 17 of 17 | NP_001341856.1 | |||
VCP | NM_001354928.2 | c.*1035delA | 3_prime_UTR_variant | Exon 17 of 17 | NP_001341857.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00271 AC: 391AN: 144392Hom.: 4 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome AF: 0.00271 AC: 391AN: 144440Hom.: 4 Cov.: 32 AF XY: 0.00330 AC XY: 231AN XY: 69954
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ClinVar
Not reported inComputational scores
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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