NM_021729.6:c.30C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_021729.6(VPS11):c.30C>T(p.Phe10Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000321 in 1,557,782 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 (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
VPS11
NM_021729.6 synonymous
NM_021729.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.08
Publications
2 publications found
Genes affected
VPS11 (HGNC:14583): (VPS11 core subunit of CORVET and HOPS complexes) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
VPS11-DT (HGNC:55227): (VPS11 divergent transcript)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BP6
Variant 11-119067853-C-T is Benign according to our data. Variant chr11-119067853-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2966844.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.08 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_021729.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VPS11 | MANE Select | c.30C>T | p.Phe10Phe | synonymous | Exon 1 of 16 | NP_068375.3 | |||
| VPS11 | c.-216C>T | 5_prime_UTR_premature_start_codon_gain | Exon 1 of 16 | NP_001277114.1 | B7Z879 | ||||
| VPS11 | c.30C>T | p.Phe10Phe | synonymous | Exon 1 of 16 | NP_001365147.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VPS11 | TSL:1 MANE Select | c.30C>T | p.Phe10Phe | synonymous | Exon 1 of 16 | ENSP00000481126.1 | A0A087WXL6 | ||
| VPS11 | TSL:2 | c.-216C>T | 5_prime_UTR_premature_start_codon_gain | Exon 1 of 16 | ENSP00000481807.1 | B7Z879 | |||
| VPS11 | c.30C>T | p.Phe10Phe | synonymous | Exon 1 of 16 | ENSP00000622584.1 |
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1405574Hom.: 0 Cov.: 31 AF XY: 0.00000144 AC XY: 1AN XY: 693768 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1405574
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
693768
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32044
American (AMR)
AF:
AC:
0
AN:
36462
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25364
East Asian (EAS)
AF:
AC:
0
AN:
36546
South Asian (SAS)
AF:
AC:
1
AN:
80286
European-Finnish (FIN)
AF:
AC:
0
AN:
49480
Middle Eastern (MID)
AF:
AC:
0
AN:
5396
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1081808
Other (OTH)
AF:
AC:
0
AN:
58188
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74364 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
152208
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
74364
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41456
American (AMR)
AF:
AC:
1
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68030
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.