rs1458836

Variant names:

• chr11-75813751-C-T
• rs1458836
• ENST00000527219.1:n.204G>A

Variant summary

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

The ENST00000531263.3(UVRAG-DT):​n.476G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,720 control chromosomes in the GnomAD database, including 3,119 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 0.17 (3119 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: UVRAG-DT ENST00000531263.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

Genes affected

UVRAG-DT (HGNC:53952): (UVRAG divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UVRAG-DT	NR_144531.1	n.446G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UVRAG-DT	ENST00000527219.1	n.204G>A		non_coding_transcript_exon_variant	Exon 2 of 4	4
UVRAG-DT	ENST00000531263.3	n.476G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
UVRAG-DT	ENST00000533590.5	n.222G>A		non_coding_transcript_exon_variant	Exon 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25676 AN: 151588 Hom.: 3110 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.142

GnomAD4 exome AF: 0.143 AC: 2 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.170 AC: 25724 AN: 151706 Hom.: 3119 Cov.: 32 AF XY: 0.166 AC XY: 12313 AN XY: 74120

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.0936

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.143

Alfa AF: 0.103 Hom.: 1947

Bravo AF: 0.179

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458836; hg19: chr11-75524796;