NM_007126.5:c.*1035delA

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839
Variant links:
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]

Genome browser will be placed here

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
VCPNM_007126.5 linkc.*1035delA 3_prime_UTR_variant Exon 17 of 17 ENST00000358901.11 NP_009057.1
VCPNM_001354927.2 linkc.*1035delA 3_prime_UTR_variant Exon 17 of 17 NP_001341856.1
VCPNM_001354928.2 linkc.*1035delA 3_prime_UTR_variant Exon 17 of 17 NP_001341857.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VCPENST00000358901 linkc.*1035delA 3_prime_UTR_variant Exon 17 of 17 1 NM_007126.5 ENSP00000351777.6 P55072

Frequencies

GnomAD3 genomes
AF:
0.00271
AC:
391
AN:
144392
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000734
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00577
Gnomad ASJ
AF:
0.000299
Gnomad EAS
AF:
0.00260
Gnomad SAS
AF:
0.0253
Gnomad FIN
AF:
0.00148
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00201
Gnomad OTH
AF:
0.00204
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.00271
AC:
391
AN:
144440
Hom.:
4
Cov.:
32
AF XY:
0.00330
AC XY:
231
AN XY:
69954
show subpopulations
Gnomad4 AFR
AF:
0.000732
Gnomad4 AMR
AF:
0.00576
Gnomad4 ASJ
AF:
0.000299
Gnomad4 EAS
AF:
0.00261
Gnomad4 SAS
AF:
0.0254
Gnomad4 FIN
AF:
0.00148
Gnomad4 NFE
AF:
0.00201
Gnomad4 OTH
AF:
0.00202
Alfa
AF:
0.000504
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs532528005; hg19: chr9-35056078; API