NM_017890.5:c.4962G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_017890.5(VPS13B):c.4962G>A(p.Gly1654Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,032 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G1654G) has been classified as Likely benign.
Frequency
Consequence
NM_017890.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.4962G>A | p.Gly1654Gly | synonymous_variant | Exon 31 of 62 | 1 | NM_017890.5 | ENSP00000351346.2 | ||
VPS13B | ENST00000357162.7 | c.4887G>A | p.Gly1629Gly | synonymous_variant | Exon 31 of 62 | 1 | NM_152564.5 | ENSP00000349685.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250512Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135366
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461032Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726826
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cohen syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at