11-119067829-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001290185.2(VPS11):c.-240G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,426 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_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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS11 | NM_021729.6 | c.6G>T | p.Ala2Ala | synonymous_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.6G>T | p.Ala2Ala | synonymous_variant | Exon 1 of 16 | 1 | NM_021729.6 | ENSP00000481126.1 | ||
VPS11 | ENST00000614944 | c.-240G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 16 | 2 | ENSP00000481807.1 | ||||
VPS11 | ENST00000614944 | c.-240G>T | 5_prime_UTR_variant | Exon 1 of 16 | 2 | ENSP00000481807.1 | ||||
VPS11 | ENST00000622309.4 | n.7G>T | non_coding_transcript_exon_variant | Exon 1 of 13 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390426Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 684122
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at