dbSNP rs6508: WT1-AS:n.1342G>A (chr11-32438918-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000395900.1(WT1-AS):n.1342G>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 0.0978 in 534,676 control chromosomes in the GnomAD database, including 5,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 3318 hom., cov: 33)

Exomes 𝑓: 0.076 ( 1736 hom. )

Consequence

WT1-AS
ENST00000395900.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.315

Publications

9 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:

ENSG00000276530 (HGNC:):

ENSG00000276530 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-32438918-G-A is Benign according to our data. Variant chr11-32438918-G-A is described in ClinVar as Benign. ClinVar VariationId is 1166184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
WT1-AS	NR_120546.1 link	n.1873G>A	non_coding_transcript_exon_variant	Exon 2 of 2
WT1-AS	NR_120547.1 link	n.1531G>A	non_coding_transcript_exon_variant	Exon 3 of 3
WT1-AS	NR_120548.1 link	n.329+3072G>A	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WT1-AS	ENST00000395900.1 link	n.1342G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
WT1-AS	ENST00000442957.1 link	n.268G>A	non_coding_transcript_exon_variant	Exon 2 of 2	3
WT1-AS	ENST00000494911.6 link	n.1531G>A	non_coding_transcript_exon_variant	Exon 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23364

AN:

152114

Hom.:

3308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.0905

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.0683

Gnomad FIN

AF:

0.0547

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.0696

Gnomad OTH

AF:

0.132

GnomAD2 exomes

AF:

0.0828

AC:

20820

AN:

251372

AF XY:

0.0774

show subpopulations

Gnomad AFR exome

AF:

0.385

Gnomad AMR exome

AF:

0.0551

Gnomad ASJ exome

AF:

0.0840

Gnomad EAS exome

AF:

0.00261

Gnomad FIN exome

AF:

0.0532

Gnomad NFE exome

AF:

0.0689

Gnomad OTH exome

AF:

0.0774

GnomAD4 exome

AF:

0.0756

AC:

28901

AN:

382444

Hom.:

1736

Cov.:

AF XY:

0.0743

AC XY:

16174

AN XY:

217716

show subpopulations

African (AFR)

AF:

0.380

AC:

4000

AN:

10514

American (AMR)

AF:

0.0563

AC:

2042

AN:

36300

Ashkenazi Jewish (ASJ)

AF:

0.0837

AC:

983

AN:

11744

East Asian (EAS)

AF:

0.00486

AC:

AN:

13176

South Asian (SAS)

AF:

0.0801

AC:

5345

AN:

66756

European-Finnish (FIN)

AF:

0.0529

AC:

1710

AN:

32318

Middle Eastern (MID)

AF:

0.114

AC:

325

AN:

2854

European-Non Finnish (NFE)

AF:

0.0679

AC:

13034

AN:

192054

Other (OTH)

AF:

0.0836

AC:

1398

AN:

16728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

2113

4226

6340

8453

10566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.154

AC:

23415

AN:

152232

Hom.:

3318

Cov.:

AF XY:

0.150

AC XY:

11183

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.379

AC:

15721

AN:

41520

American (AMR)

AF:

0.0904

AC:

1383

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

246

AN:

3470

East Asian (EAS)

AF:

0.0100

AC:

AN:

5180

South Asian (SAS)

AF:

0.0683

AC:

330

AN:

4830

European-Finnish (FIN)

AF:

0.0547

AC:

580

AN:

10612

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0696

AC:

4734

AN:

68006

Other (OTH)

AF:

0.130

AC:

274

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

887

1775

2662

3550

4437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.104

Hom.:

2615

Bravo

AF:

0.165

Asia WGS

AF:

0.0590

AC:

206

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

11p partial monosomy syndrome;C0950121:Drash syndrome;C0950122:Frasier syndrome;CN033288:Wilms tumor 1

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.3

(source)

DANN

Benign

0.71

PhyloP100

-0.32

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

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over