NM_017890.5:c.5024+34T>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_017890.5(VPS13B):c.5024+34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000987 in 1,600,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000093 ( 0 hom. )
Consequence
VPS13B
NM_017890.5 intron
NM_017890.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.808
Publications
0 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: Likely_benign. The variant received -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 8-99556687-T-C is Benign according to our data. Variant chr8-99556687-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 262662.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.5024+34T>C | intron_variant | Intron 31 of 61 | 1 | NM_017890.5 | ENSP00000351346.2 | |||
VPS13B | ENST00000357162.7 | c.4949+34T>C | intron_variant | Intron 31 of 61 | 1 | NM_152564.5 | ENSP00000349685.2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152192Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
24
AN:
152192
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:
GnomAD2 exomes AF: 0.000304 AC: 71AN: 233708 AF XY: 0.000278 show subpopulations
GnomAD2 exomes
AF:
AC:
71
AN:
233708
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000925 AC: 134AN: 1448522Hom.: 0 Cov.: 29 AF XY: 0.000101 AC XY: 73AN XY: 719884 show subpopulations
GnomAD4 exome
AF:
AC:
134
AN:
1448522
Hom.:
Cov.:
29
AF XY:
AC XY:
73
AN XY:
719884
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33236
American (AMR)
AF:
AC:
0
AN:
43446
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25804
East Asian (EAS)
AF:
AC:
117
AN:
39458
South Asian (SAS)
AF:
AC:
3
AN:
84504
European-Finnish (FIN)
AF:
AC:
0
AN:
52868
Middle Eastern (MID)
AF:
AC:
1
AN:
5722
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1103566
Other (OTH)
AF:
AC:
13
AN:
59918
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
8
16
24
32
40
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.000158 AC: 24AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74478 show subpopulations
GnomAD4 genome
AF:
AC:
24
AN:
152310
Hom.:
Cov.:
32
AF XY:
AC XY:
15
AN XY:
74478
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41582
American (AMR)
AF:
AC:
0
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
22
AN:
5186
South Asian (SAS)
AF:
AC:
1
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68014
Other (OTH)
AF:
AC:
1
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.462
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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