chr11-119067905-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021729.6(VPS11):c.82G>A(p.Ala28Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,602,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A28A) has been classified as Likely benign.
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS11 | NM_021729.6 | c.82G>A | p.Ala28Thr | missense_variant | 1/16 | ENST00000621676.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS11 | ENST00000621676.5 | c.82G>A | p.Ala28Thr | missense_variant | 1/16 | 1 | NM_021729.6 | P1 | |
VPS11 | ENST00000614944.4 | c.-164G>A | 5_prime_UTR_variant | 1/16 | 2 | ||||
VPS11 | ENST00000622309.4 | n.83G>A | non_coding_transcript_exon_variant | 1/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450426Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 720514
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.82G>A (p.A28T) 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 82, causing the alanine (A) at amino acid position 28 to be replaced by a threonine (T). 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