X-155239176-T-G

Variant names:

• chrX-155239176-T-G
• rs11887
• NM_003372.7:c.*334T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003372.7(VBP1):​c.*334T>G variant causes a 3 prime UTR 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: not found (cov: 23)
• Consequence: VBP1 NM_003372.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 11 publications found

Genes affected

VBP1 (HGNC:12662): (VHL binding protein 1) The protein encoded by this gene interacts with the Von Hippel-Lindau protein to form an intracellular complex. The encoded protein functions as a chaperone protein, and may play a role in the transport of the Von Hippel-Lindau protein from the perinuclear granules to the nucleus or cytoplasm. Alternative splicing and the use of alternate transcription start sites results in multiple transcript variants encoding different protein isoforms. [provided by RefSeq, Jan 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003372.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VBP1	NM_003372.7	MANE Select	c.*334T>G		3_prime_UTR	Exon 6 of 6	NP_003363.1	P61758-1
	VBP1	NM_001303543.1		c.*334T>G		3_prime_UTR	Exon 6 of 6	NP_001290472.1	P61758
	VBP1	NM_001303544.1		c.*334T>G		3_prime_UTR	Exon 7 of 7	NP_001290473.1	P61758-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VBP1	ENST00000286428.7	TSL:1 MANE Select	c.*334T>G		3_prime_UTR	Exon 6 of 6	ENSP00000286428.5	P61758-1
	VBP1	ENST00000926244.1		c.*334T>G		3_prime_UTR	Exon 6 of 6	ENSP00000596303.1
	VBP1	ENST00000971683.1		c.*334T>G		3_prime_UTR	Exon 6 of 6	ENSP00000641742.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
PhyloP100		0.50

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

Other links and lift over

dbSNP: rs11887; hg19: chrX-154467457;