11-76121878-G-A

Variant names:

• chr11-76121878-G-A
• rs17134573
• NM_003369.4:c.1397+5863G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UVRAG	NM_003369.4	MANE Select	c.1397+5863G>A		intron	N/A	NP_003360.2
	UVRAG	NM_001386671.1		c.1397+5863G>A		intron	N/A	NP_001373600.1
	UVRAG	NM_001386672.1		c.1235+5863G>A		intron	N/A	NP_001373601.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UVRAG	ENST00000356136.8	TSL:1 MANE Select	c.1397+5863G>A		intron	N/A	ENSP00000348455.3
	UVRAG	ENST00000528420.5	TSL:2	c.1094+5863G>A		intron	N/A	ENSP00000436039.1
	UVRAG	ENST00000531818.5	TSL:2	c.281+5863G>A		intron	N/A	ENSP00000434082.1

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

African (AFR) AF: 0.282 AC: 11682 AN: 41450

American (AMR) AF: 0.0400 AC: 612 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.00733 AC: 38 AN: 5186

South Asian (SAS) AF: 0.0416 AC: 201 AN: 4826

European-Finnish (FIN) AF: 0.0201 AC: 213 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0298 AC: 2025 AN: 68024

Other (OTH) AF: 0.0701 AC: 148 AN: 2110

Alfa AF: 0.0356 Hom.: 162

Bravo AF: 0.108

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.086
DANN	Benign	0.53
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17134573; hg19: chr11-75832922;