rs7116263

chr11-76015744-C-Gchr11-76015744-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003369.4(UVRAG):c.1061-1071C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,998 control chromosomes in the GnomAD database, including 5,064 homozygotes. 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: Genomes: 𝑓 0.20 (5064 hom., cov: 32)
• Consequence: UVRAG NM_003369.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UVRAG	NM_003369.4	c.1061-1071C>G		intron_variant		ENST00000356136.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UVRAG	ENST00000356136.8	c.1061-1071C>G		intron_variant		1	NM_003369.4	P2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29630 AN: 151880 Hom.: 5041 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.195 AC: 29706 AN: 151998 Hom.: 5064 Cov.: 32 AF XY: 0.192 AC XY: 14282 AN XY: 74284

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.0932

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0786

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0653 Hom.: 102

Bravo AF: 0.204

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.2
Dann	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7116263; hg19: chr11-75726788;