rs184381851
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_017890.5(VPS13B):c.9405+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,611,106 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0025 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
VPS13B
NM_017890.5 intron
NM_017890.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.267
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-99823987-A-G is Benign according to our data. Variant chr8-99823987-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 130729.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-99823987-A-G is described in Lovd as [Benign]. Variant chr8-99823987-A-G is described in Lovd as [Likely_benign].
BS2
?
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.9405+9A>G | intron_variant | ENST00000358544.7 | |||
VPS13B | NM_152564.5 | c.9330+9A>G | intron_variant | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000357162.7 | c.9330+9A>G | intron_variant | 1 | NM_152564.5 | P1 | |||
VPS13B | ENST00000358544.7 | c.9405+9A>G | intron_variant | 1 | NM_017890.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00241 AC: 367AN: 152210Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000636 AC: 158AN: 248556Hom.: 0 AF XY: 0.000527 AC XY: 71AN XY: 134706
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GnomAD4 exome AF: 0.000235 AC: 343AN: 1458778Hom.: 2 Cov.: 31 AF XY: 0.000201 AC XY: 146AN XY: 725830
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Cohen syndrome Benign:4
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 06, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jul 06, 2017 | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 27, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 03, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at