rs147342579
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017890.5(VPS13B):c.4832A>G(p.Asn1611Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,612,618 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. N1611H) has been classified as Uncertain significance.
Frequency
Consequence
NM_017890.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.4832A>G | p.Asn1611Ser | missense_variant | 31/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.4757A>G | p.Asn1586Ser | missense_variant | 31/62 | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.4832A>G | p.Asn1611Ser | missense_variant | 31/62 | 1 | NM_017890.5 | ||
VPS13B | ENST00000357162.7 | c.4757A>G | p.Asn1586Ser | missense_variant | 31/62 | 1 | NM_152564.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 249912Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135144
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460542Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 726598
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 23AN XY: 74272
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 05, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Sep 16, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 03, 2015 | - - |
Cohen syndrome Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 29, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at