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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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 id 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	ENST00000525436.1 link	n.46+3072G>A	intron_variant	Intron 1 of 4	5

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

GnomAD3 exomes

AF:

0.0828

AC:

20820

AN:

251372

Hom.:

1748

AF XY:

0.0774

AC XY:

10514

AN XY:

135878

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 SAS exome

AF:

0.0758

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

Gnomad4 AFR exome

AF:

0.380

Gnomad4 AMR exome

AF:

0.0563

Gnomad4 ASJ exome

AF:

0.0837

Gnomad4 EAS exome

AF:

0.00486

Gnomad4 SAS exome

AF:

0.0801

Gnomad4 FIN exome

AF:

0.0529

Gnomad4 NFE exome

AF:

0.0679

Gnomad4 OTH exome

AF:

0.0836

GnomAD4 genome

AF:

0.154

AC:

23415

AN:

152232

Hom.:

3318

Cov.:

AF XY:

0.150

AC XY:

11183

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.0904

Gnomad4 ASJ

AF:

0.0709

Gnomad4 EAS

AF:

0.0100

Gnomad4 SAS

AF:

0.0683

Gnomad4 FIN

AF:

0.0547

Gnomad4 NFE

AF:

0.0696

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0950

Hom.:

1604

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

DANN

Benign

0.71

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over