X-155216554-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003372.7(VBP1):c.72G>T(p.Gly24=) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
VBP1
NM_003372.7 synonymous
NM_003372.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.287
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant X-155216554-G-T is Benign according to our data. Variant chrX-155216554-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661875.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.287 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VBP1 | NM_003372.7 | c.72G>T | p.Gly24= | synonymous_variant | 1/6 | ENST00000286428.7 | |
VBP1 | NM_001303543.1 | c.180G>T | p.Gly60= | synonymous_variant | 1/6 | ||
VBP1 | NM_001303545.1 | c.-36G>T | 5_prime_UTR_variant | 1/6 | |||
VBP1 | NM_001303544.1 | c.79-3629G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VBP1 | ENST00000286428.7 | c.72G>T | p.Gly24= | synonymous_variant | 1/6 | 1 | NM_003372.7 | P1 | |
VBP1 | ENST00000535916.5 | c.79-3629G>T | intron_variant | 2 | |||||
VBP1 | ENST00000625964.2 | c.79-3629G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1055927Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 345269
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1055927
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
345269
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | VBP1: PM2:Supporting, BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.