NM_017890.5:c.3871-2934G>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017890.5(VPS13B):c.3871-2934G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,082 control chromosomes in the GnomAD database, including 449 homozygotes. 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: 𝑓 0.065 ( 449 hom., cov: 32)
Consequence
VPS13B
NM_017890.5 intron
NM_017890.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.63
Publications
2 publications found
Genes affected
VPS13B (HGNC:2183): (vacuolar protein sorting 13 homolog B) This gene encodes a potential transmembrane protein that may function in vesicle-mediated transport and sorting of proteins within the cell. This protein may play a role in the development and the function of the eye, hematological system, and central nervous system. Mutations in this gene have been associated with Cohen syndrome. Multiple splice variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
VPS13B Gene-Disease associations (from GenCC):
- Cohen syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Myriad Women’s Health, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Laboratory for Molecular Medicine, ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.3871-2934G>C | intron_variant | Intron 25 of 61 | 1 | NM_017890.5 | ENSP00000351346.2 | |||
VPS13B | ENST00000357162.7 | c.3871-2934G>C | intron_variant | Intron 25 of 61 | 1 | NM_152564.5 | ENSP00000349685.2 |
Frequencies
GnomAD3 genomes AF: 0.0651 AC: 9895AN: 151962Hom.: 444 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
9895
AN:
151962
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0653 AC: 9926AN: 152082Hom.: 449 Cov.: 32 AF XY: 0.0656 AC XY: 4876AN XY: 74362 show subpopulations
GnomAD4 genome
AF:
AC:
9926
AN:
152082
Hom.:
Cov.:
32
AF XY:
AC XY:
4876
AN XY:
74362
show subpopulations
African (AFR)
AF:
AC:
5197
AN:
41484
American (AMR)
AF:
AC:
841
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
62
AN:
3470
East Asian (EAS)
AF:
AC:
314
AN:
5180
South Asian (SAS)
AF:
AC:
105
AN:
4826
European-Finnish (FIN)
AF:
AC:
471
AN:
10588
Middle Eastern (MID)
AF:
AC:
7
AN:
294
European-Non Finnish (NFE)
AF:
AC:
2812
AN:
67960
Other (OTH)
AF:
AC:
108
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
462
924
1385
1847
2309
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
201
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
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