rs2301252

Positions:

• chr11-32436381-C-A
• chr11-32436381-C-G

Variant summary

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

The ENST00000613208.1(ENSG00000273677):​n.71C>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 0.484 in 152,242 control chromosomes in the GnomAD database, including 19,683 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 0.48 (19652 hom., cov: 33)
  • Exomes 𝑓: 0.52 (31 hom.)
• Consequence: ENST00000613208.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

(HGNC:):

WT1-AS (HGNC:18135): (WT1 antisense RNA) This gene is located upstream of the Wilms tumor 1 (WT1) gene; these two genes are bi-directionally transcribed from the same promoter region. This gene is imprinted in kidney, with preferential expression from the paternal allele. Imprinting defects at chromosome 11p13 may contribute to tumorigenesis. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WT1-AS	NR_120548.1	n.329+535C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000613208.1	n.71C>A		non_coding_transcript_exon_variant	1/1
WT1-AS	ENST00000690579.1	n.225+535C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73485 AN: 151886 Hom.: 19603 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.517 AC: 123 AN: 238 Hom.: 31 Cov.: 0 AF XY: 0.512 AC XY: 85 AN XY: 166

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.490

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.484 AC: 73587 AN: 152004 Hom.: 19652 Cov.: 33 AF XY: 0.488 AC XY: 36261 AN XY: 74290

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.509

Alfa AF: 0.345 Hom.: 1285

Bravo AF: 0.502

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2301252; hg19: chr11-32457927;