rs979238008
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021729.6(VPS11):āc.13C>Gā(p.Leu5Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000215 in 1,397,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_021729.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS11 | NM_021729.6 | c.13C>G | p.Leu5Val | missense_variant | Exon 1 of 16 | ENST00000621676.5 | NP_068375.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS11 | ENST00000621676.5 | c.13C>G | p.Leu5Val | missense_variant | Exon 1 of 16 | 1 | NM_021729.6 | ENSP00000481126.1 | ||
VPS11 | ENST00000614944 | c.-233C>G | 5_prime_UTR_variant | Exon 1 of 16 | 2 | ENSP00000481807.1 | ||||
VPS11 | ENST00000622309.4 | n.14C>G | non_coding_transcript_exon_variant | Exon 1 of 13 | 5 | |||||
VPS11-DT | ENST00000607709.1 | n.-138G>C | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000622 AC: 1AN: 160696Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 85572
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1397238Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 688538
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at