rs201136777
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_017890.5(VPS13B):c.4821-7T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,612,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017890.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.4821-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000358544.7 | |||
VPS13B | NM_152564.5 | c.4746-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000357162.7 | c.4746-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_152564.5 | P1 | |||
VPS13B | ENST00000358544.7 | c.4821-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_017890.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000764 AC: 19AN: 248784Hom.: 0 AF XY: 0.0000669 AC XY: 9AN XY: 134612
GnomAD4 exome AF: 0.000149 AC: 217AN: 1459946Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 98AN XY: 726254
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74428
ClinVar
Submissions by phenotype
Cohen syndrome Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 29, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
VPS13B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 28, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at