rs1458836

Variant names:

• chr11-75813751-C-T
• rs1458836
• ENST00000525580.2:n.730G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525580.2(UVRAG-DT):​n.730G>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 ENST00000525580.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 15 publications found

Genes affected

UVRAG-DT (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525580.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UVRAG-DT	NR_144531.1		n.446G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UVRAG-DT	ENST00000525580.2	TSL:2	n.730G>A		non_coding_transcript_exon	Exon 2 of 4
	UVRAG-DT	ENST00000527219.1	TSL:4	n.204G>A		non_coding_transcript_exon	Exon 2 of 4
	UVRAG-DT	ENST00000531263.4	TSL:2	n.750G>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 2 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.341 AC: 14087 AN: 41276

American (AMR) AF: 0.124 AC: 1886 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5168

South Asian (SAS) AF: 0.0936 AC: 451 AN: 4818

European-Finnish (FIN) AF: 0.0732 AC: 766 AN: 10464

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6513 AN: 67974

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.118 Hom.: 4457

Bravo AF: 0.179

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1458836;

hg19: chr11-75524796;