8-99106959-G-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.580+3839G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 151,974 control chromosomes in the GnomAD database, including 41,771 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 0.73 ( 41771 hom., cov: 31)
Consequence
VPS13B
NM_017890.5 intron
NM_017890.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.252
Publications
1 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 (SAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.580+3839G>C | intron_variant | Intron 5 of 61 | 1 | NM_017890.5 | ENSP00000351346.2 | |||
VPS13B | ENST00000357162.7 | c.580+3839G>C | intron_variant | Intron 5 of 61 | 1 | NM_152564.5 | ENSP00000349685.2 |
Frequencies
GnomAD3 genomes AF: 0.735 AC: 111653AN: 151856Hom.: 41766 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
111653
AN:
151856
Hom.:
Cov.:
31
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: 0.735 AC: 111696AN: 151974Hom.: 41771 Cov.: 31 AF XY: 0.733 AC XY: 54446AN XY: 74282 show subpopulations
GnomAD4 genome
AF:
AC:
111696
AN:
151974
Hom.:
Cov.:
31
AF XY:
AC XY:
54446
AN XY:
74282
show subpopulations
African (AFR)
AF:
AC:
27410
AN:
41410
American (AMR)
AF:
AC:
9235
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
2859
AN:
3470
East Asian (EAS)
AF:
AC:
2927
AN:
5170
South Asian (SAS)
AF:
AC:
4174
AN:
4818
European-Finnish (FIN)
AF:
AC:
8365
AN:
10554
Middle Eastern (MID)
AF:
AC:
247
AN:
292
European-Non Finnish (NFE)
AF:
AC:
54193
AN:
67986
Other (OTH)
AF:
AC:
1545
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1440
2880
4320
5760
7200
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
846
1692
2538
3384
4230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2381
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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