NM_007126.5:c.1082-18_1082-8delTTGTGTACTGT

Variant names:

• chr9-35061696-GACAGTACACAA-G
• NM_007126.5:c.1082-18_1082-8delTTGTGTACTGT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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]

ACMG classification

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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VCP	NM_007126.5	c.1082-18_1082-8delTTGTGTACTGT		splice_region_variant, intron_variant	Intron 9 of 16	ENST00000358901.11	NP_009057.1
VCP	NM_001354927.2	c.947-18_947-8delTTGTGTACTGT		splice_region_variant, intron_variant	Intron 9 of 16		NP_001341856.1
VCP	NM_001354928.2	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	c.1082-18_1082-8delTTGTGTACTGT		splice_region_variant, intron_variant	Intron 9 of 16	1	NM_007126.5	ENSP00000351777.6

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-35061693;