rs594826

Variant names:

• chr11-76045630-G-A
• rs594826
• NM_003369.4:c.1227-20080G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-76045630-G-A
• chr11-76045630-G-C
• chr11-76045630-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.1227-20080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 150,086 control chromosomes in the GnomAD database, including 371 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 0.056 (371 hom., cov: 31)
• Consequence: UVRAG NM_003369.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UVRAG	NM_003369.4	c.1227-20080G>A		intron_variant	Intron 12 of 14	ENST00000356136.8	NP_003360.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UVRAG	ENST00000356136.8	c.1227-20080G>A		intron_variant	Intron 12 of 14	1	NM_003369.4	ENSP00000348455.3

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8476 AN: 149968 Hom.: 372 Cov.: 31

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0460

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0564 AC: 8464 AN: 150086 Hom.: 371 Cov.: 31 AF XY: 0.0602 AC XY: 4396 AN XY: 73072

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.0493

Gnomad4 ASJ AF: 0.0460

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0863

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0630

Alfa AF: 0.0521 Hom.: 69

Bravo AF: 0.0533

Asia WGS AF: 0.139 AC: 484 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.65

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: rs594826; hg19: chr11-75756674;