11-119067875-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001290185.2(VPS11):c.-194G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000146 in 1,577,222 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001290185.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS11 | NM_021729.6 | c.52G>A | p.Val18Met | 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.52G>A | p.Val18Met | missense_variant | Exon 1 of 16 | 1 | NM_021729.6 | ENSP00000481126.1 | ||
VPS11 | ENST00000614944 | c.-194G>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 16 | 2 | ENSP00000481807.1 | ||||
VPS11 | ENST00000614944 | c.-194G>A | 5_prime_UTR_variant | Exon 1 of 16 | 2 | ENSP00000481807.1 | ||||
VPS11 | ENST00000622309.4 | n.53G>A | non_coding_transcript_exon_variant | Exon 1 of 13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152254Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000491 AC: 7AN: 1424968Hom.: 0 Cov.: 31 AF XY: 0.00000425 AC XY: 3AN XY: 705658
GnomAD4 genome AF: 0.000105 AC: 16AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74386
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.52G>A (p.V18M) alteration is located in exon 1 (coding exon 1) of the VPS11 gene. This alteration results from a G to A substitution at nucleotide position 52, causing the valine (V) at amino acid position 18 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at