rs2301250

chr11-32436673-G-A

Variant summary

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

The NR_120548.1(WT1-AS):n.329+827G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,878 control chromosomes in the GnomAD database, including 19,629 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 (19619 hom., cov: 32)
  • Exomes 𝑓: 0.48 (10 hom.)
• Consequence: WT1-AS NR_120548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WT1-AS	NR_120548.1	n.329+827G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WT1-AS	ENST00000690579.1	n.225+827G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73380 AN: 151706 Hom.: 19570 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.481 AC: 26 AN: 54 Hom.: 10 AF XY: 0.432 AC XY: 19 AN XY: 44

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.457

GnomAD4 genome AF: 0.484 AC: 73482 AN: 151824 Hom.: 19619 Cov.: 32 AF XY: 0.488 AC XY: 36203 AN XY: 74176

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.508

Alfa AF: 0.394 Hom.: 16082

Bravo AF: 0.503

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.7
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2301250; hg19: chr11-32458219;