rs2301254

Variant names:

• chr11-32436129-A-G
• rs2301254
• ENST00000686872.2:n.504A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-32436129-A-G
• chr11-32436129-A-T

Variant summary

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

The ENST00000686872.2(WT1-AS):​n.504A>G 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 151,866 control chromosomes in the GnomAD database, including 19,618 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 (19618 hom., cov: 31)
• Consequence: WT1-AS ENST00000686872.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 7 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]

ENSG00000273677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt
WT1-AS	NR_120546.1	n.91A>G		non_coding_transcript_exon_variant	Exon 1 of 2
WT1-AS	NR_023920.2	n.329+283A>G		intron_variant	Intron 1 of 1
WT1-AS	NR_120547.1	n.329+283A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WT1-AS	ENST00000686872.2	n.504A>G		non_coding_transcript_exon_variant	Exon 1 of 1
WT1-AS	ENST00000395900.1	n.268+283A>G		intron_variant	Intron 1 of 1	2
WT1-AS	ENST00000459866.2	n.300+283A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73399 AN: 151750 Hom.: 19570 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.502

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.484 AC: 73499 AN: 151866 Hom.: 19618 Cov.: 31 AF XY: 0.488 AC XY: 36226 AN XY: 74232

African (AFR) AF: 0.684 AC: 28317 AN: 41422

American (AMR) AF: 0.494 AC: 7538 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1378 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3870 AN: 5142

South Asian (SAS) AF: 0.644 AC: 3089 AN: 4798

European-Finnish (FIN) AF: 0.318 AC: 3350 AN: 10526

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24456 AN: 67926

Other (OTH) AF: 0.509 AC: 1072 AN: 2108

Alfa AF: 0.428 Hom.: 1980

Bravo AF: 0.502

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	-0.88
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2301254; hg19: chr11-32457675;