Genetic Variant ENST00000686872.2:n.1048G>A (chr11-32436673-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000686872.2(WT1-AS):n.1048G>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
ENST00000686872.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.138

Publications

8 publications found

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 was made for transcript

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.

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	ENST00000686872.2 link	n.1048G>A	non_coding_transcript_exon_variant	Exon 1 of 1
WT1-AS	ENST00000813668.1 link	n.193G>A	non_coding_transcript_exon_variant	Exon 1 of 2
WT1-AS	ENST00000395900.1 link	n.268+827G>A	intron_variant	Intron 1 of 1	2

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

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.457

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.484

AC:

73482

AN:

151824

Hom.:

19619

Cov.:

AF XY:

0.488

AC XY:

36203

AN XY:

74176

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1721

3442

5163

6884

8605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.7

(source)

DANN

Benign

0.74

PhyloP100

0.14

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over