dbSNP rs2301250: WT1-AS:n.876G>A (chr11-32436673-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.138

Variant links:

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]

WT1-AS links:

ENSG00000278045 (HGNC:):

ENSG00000278045 links:

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ACMG classification

Classification made for transcript

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	Effect	Exon rank
WT1-AS	NR_120546.1 link	n.635G>A	non_coding_transcript_exon_variant	Exon 1 of 2
WT1-AS	NR_023920.2 link	n.329+827G>A	intron_variant	Intron 1 of 1
WT1-AS	NR_120547.1 link	n.330-397G>A	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WT1-AS	ENST00000686872.1 link	n.876G>A	non_coding_transcript_exon_variant	Exon 1 of 1
WT1-AS	ENST00000395900.1 link	n.268+827G>A	intron_variant	Intron 1 of 1	2
WT1-AS	ENST00000459866.1 link	n.72-122G>A	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73380

AN:

151706

Hom.:

19570

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.432

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.488

AC XY:

36203

AN XY:

74176

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over