dbSNP rs11272867: VCP:c.1082-18_1082-8delTTGTGTACTGT (chr9-35061696-GACAGTACACAA-G) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_007126.5(VCP):c.1082-18_1082-8delTTGTGTACTGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: not found (cov: 0)

Consequence

VCP
NM_007126.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

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]

VCP links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP6

Variant 9-35061696-GACAGTACACAA-G is Benign according to our data. Variant chr9-35061696-GACAGTACACAA-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
VCP	NM_007126.5 link	c.1082-18_1082-8delTTGTGTACTGT	splice_region_variant, intron_variant	Intron 9 of 16	ENST00000358901.11	NP_009057.1
VCP	NM_001354927.2 link	c.947-18_947-8delTTGTGTACTGT	splice_region_variant, intron_variant	Intron 9 of 16		NP_001341856.1
VCP	NM_001354928.2 link	c.947-18_947-8delTTGTGTACTGT	splice_region_variant, intron_variant	Intron 9 of 16		NP_001341857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VCP	ENST00000358901.11 link	c.1082-18_1082-8delTTGTGTACTGT		splice_region_variant, intron_variant	Intron 9 of 16	1	NM_007126.5	ENSP00000351777.6		P55072

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.