rs2301250

Variant names:

• chr11-32436673-G-A
• rs2301250
• ENST00000686872.2:n.1048G>A

Variant summary

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

The NR_120546.1(WT1-AS):​n.635G>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 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_120546.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 8 publications found

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]

ENSG00000278045 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120546.1. 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
	WT1-AS	NR_120546.1		n.635G>A		non_coding_transcript_exon	Exon 1 of 2
	WT1-AS	NR_023920.2		n.329+827G>A		intron	N/A
	WT1-AS	NR_120547.1		n.330-397G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WT1-AS	ENST00000686872.2		n.1048G>A		non_coding_transcript_exon	Exon 1 of 1
	WT1-AS	ENST00000813668.1		n.193G>A		non_coding_transcript_exon	Exon 1 of 2
	WT1-AS	ENST00000395900.1	TSL:2	n.268+827G>A		intron	N/A

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

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

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: 0.457 AC: 21 AN: 46

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.684 AC: 28314 AN: 41386

American (AMR) AF: 0.494 AC: 7543 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3466

East Asian (EAS) AF: 0.753 AC: 3838 AN: 5098

South Asian (SAS) AF: 0.643 AC: 3095 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3354 AN: 10528

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24467 AN: 67962

Other (OTH) AF: 0.508 AC: 1068 AN: 2102

Alfa AF: 0.417 Hom.: 34143

Bravo AF: 0.503

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2301250; hg19: chr11-32458219;