chr11-119067829-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_021729.6(VPS11):c.6G>A(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,542,676 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. A2A) has been classified as Likely benign.
Frequency
Consequence
NM_021729.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS11 | NM_021729.6 | c.6G>A | p.Ala2= | synonymous_variant | 1/16 | ENST00000621676.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS11 | ENST00000621676.5 | c.6G>A | p.Ala2= | synonymous_variant | 1/16 | 1 | NM_021729.6 | P1 | |
VPS11 | ENST00000614944.4 | c.-240G>A | 5_prime_UTR_variant | 1/16 | 2 | ||||
VPS11 | ENST00000622309.4 | n.7G>A | non_coding_transcript_exon_variant | 1/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000191 AC: 3AN: 156904Hom.: 0 AF XY: 0.0000359 AC XY: 3AN XY: 83456
GnomAD4 exome AF: 0.0000151 AC: 21AN: 1390428Hom.: 0 Cov.: 31 AF XY: 0.0000102 AC XY: 7AN XY: 684124
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at