rs1554581821
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_017890.5(VPS13B):c.10847_10849del(p.Phe3616del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. S3615S) has been classified as Likely benign.
Frequency
Consequence
NM_017890.5 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.10847_10849del | p.Phe3616del | inframe_deletion | 56/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.10772_10774del | p.Phe3591del | inframe_deletion | 56/62 | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000357162.7 | c.10772_10774del | p.Phe3591del | inframe_deletion | 56/62 | 1 | NM_152564.5 | P1 | |
VPS13B | ENST00000358544.7 | c.10847_10849del | p.Phe3616del | inframe_deletion | 56/62 | 1 | NM_017890.5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461696Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727148
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cohen syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Sep 29, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at