rs61753722
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017890.5(VPS13B):c.3203C>T(p.Thr1068Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00933 in 1,611,946 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1068P) has been classified as Uncertain significance.
Frequency
Consequence
NM_017890.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.3203C>T | p.Thr1068Ile | missense_variant | 22/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.3203C>T | p.Thr1068Ile | missense_variant | 22/62 | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.3203C>T | p.Thr1068Ile | missense_variant | 22/62 | 1 | NM_017890.5 | ||
VPS13B | ENST00000357162.7 | c.3203C>T | p.Thr1068Ile | missense_variant | 22/62 | 1 | NM_152564.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00791 AC: 1204AN: 152142Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.0105 AC: 2621AN: 249926Hom.: 33 AF XY: 0.0122 AC XY: 1646AN XY: 135236
GnomAD4 exome AF: 0.00948 AC: 13841AN: 1459686Hom.: 139 Cov.: 31 AF XY: 0.0103 AC XY: 7503AN XY: 726188
GnomAD4 genome AF: 0.00790 AC: 1203AN: 152260Hom.: 11 Cov.: 32 AF XY: 0.00850 AC XY: 633AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2019 | This variant is associated with the following publications: (PMID: 29758347) - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 29, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 30, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | VPS13B: BS1, BS2 - |
Cohen syndrome Benign:4
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 06, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 18, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 30, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 02, 2014 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at