rs17134573

chr11-76121878-G-Achr11-76121878-G-T

Variant summary

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

The NM_003369.4(UVRAG):c.1397+5863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,156 control chromosomes in the GnomAD database, including 1,736 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 0.099 (1736 hom., cov: 32)
• Consequence: UVRAG NM_003369.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UVRAG	NM_003369.4	c.1397+5863G>A		intron_variant		ENST00000356136.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UVRAG	ENST00000356136.8	c.1397+5863G>A		intron_variant		1	NM_003369.4	P2

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14973 AN: 152038 Hom.: 1725 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00731

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0987 AC: 15018 AN: 152156 Hom.: 1736 Cov.: 32 AF XY: 0.0945 AC XY: 7028 AN XY: 74404

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.00733

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0354 Hom.: 149

Bravo AF: 0.108

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.086
Dann	Benign	0.53

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: rs17134573; hg19: chr11-75832922;