rs141638933
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_017890.5(VPS13B):āc.2377C>Gā(p.Leu793Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000297 in 1,613,466 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L793P) has been classified as Uncertain significance.
Frequency
Consequence
NM_017890.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.2377C>G | p.Leu793Val | missense_variant | 17/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.2377C>G | p.Leu793Val | missense_variant | 17/62 | ENST00000357162.7 | |
VPS13B | NM_015243.3 | c.2377C>G | p.Leu793Val | missense_variant | 17/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.2377C>G | p.Leu793Val | missense_variant | 17/62 | 1 | NM_017890.5 | ||
VPS13B | ENST00000357162.7 | c.2377C>G | p.Leu793Val | missense_variant | 17/62 | 1 | NM_152564.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251006Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135692
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461236Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726928
GnomAD4 genome AF: 0.000210 AC: 32AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74430
ClinVar
Submissions by phenotype
Cohen syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jul 19, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
VPS13B-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 19, 2023 | The VPS13B c.2377C>G variant is predicted to result in the amino acid substitution p.Leu793Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.060% of alleles in individuals of African descent in gnomAD, which is likely too common for an undocumented cause of disease. Although we suspect that this variant may be benign, at this time, the clinical significance is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 04, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at