chr11-75983402-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_003369.4(UVRAG):c.715T>C(p.Cys239Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000693 in 1,442,560 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
UVRAG
NM_003369.4 missense
NM_003369.4 missense
Scores
1
9
8
Clinical Significance
Conservation
PhyloP100: 5.31
Publications
0 publications found
Genes affected
UVRAG (HGNC:12640): (UV radiation resistance associated) This gene complements the ultraviolet sensitivity of xeroderma pigmentosum group C cells and encodes a protein with a C2 domain. The protein activates the Beclin1-PI(3)KC3 complex, promoting autophagy and suppressing the proliferation and tumorigenicity of human colon cancer cells. Chromosomal aberrations involving this gene are associated with left-right axis malformation and mutations in this gene have been associated with colon cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003369.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| UVRAG | TSL:1 MANE Select | c.715T>C | p.Cys239Arg | missense | Exon 8 of 15 | ENSP00000348455.3 | Q9P2Y5-1 | ||
| UVRAG | c.715T>C | p.Cys239Arg | missense | Exon 8 of 16 | ENSP00000547011.1 | ||||
| UVRAG | c.715T>C | p.Cys239Arg | missense | Exon 8 of 15 | ENSP00000639525.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1442560Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 716054 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1442560
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
716054
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32514
American (AMR)
AF:
AC:
0
AN:
41602
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25608
East Asian (EAS)
AF:
AC:
0
AN:
39512
South Asian (SAS)
AF:
AC:
0
AN:
81154
European-Finnish (FIN)
AF:
AC:
0
AN:
53060
Middle Eastern (MID)
AF:
AC:
0
AN:
5658
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1103910
Other (OTH)
AF:
AC:
0
AN:
59542
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
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
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of MoRF binding (P = 6e-04)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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
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