chr11-32434893-C-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBS2_Supporting

The NM_024426.6(WT1):c.468G>T(p.Pro156Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P156P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000075 ( 0 hom. )

Consequence

WT1
NM_024426.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.141

Publications

0 publications found

Variant links:

Genes affected

WT1 (HGNC:12796): (WT1 transcription factor) This gene encodes a transcription factor that contains four zinc-finger motifs at the C-terminus and a proline/glutamine-rich DNA-binding domain at the N-terminus. It has an essential role in the normal development of the urogenital system, and it is mutated in a small subset of patients with Wilms tumor. This gene exhibits complex tissue-specific and polymorphic imprinting pattern, with biallelic, and monoallelic expression from the maternal and paternal alleles in different tissues. Multiple transcript variants have been described. In several variants, there is evidence for the use of a non-AUG (CUG) translation initiation codon upstream of, and in-frame with the first AUG. Authors of PMID:7926762 also provide evidence that WT1 mRNA undergoes RNA editing in human and rat, and that this process is tissue-restricted and developmentally regulated. [provided by RefSeq, Mar 2015]

WT1 Gene-Disease associations (from GenCC):

Denys-Drash syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, G2P
Wilms tumor 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae)
familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Frasier syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

WT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 11-32434893-C-A is Benign according to our data. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32434893-C-A is described in CliVar as Likely_benign. Clinvar id is 414079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAdExome4 at 11 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WT1	NM_024426.6 link	c.468G>T	p.Pro156Pro	synonymous_variant	Exon 1 of 10	ENST00000452863.10	NP_077744.4	P19544-7Q6PI38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WT1	ENST00000452863.10 link	c.468G>T	p.Pro156Pro	synonymous_variant	Exon 1 of 10	1	NM_024426.6	ENSP00000415516.5		P19544-7A0A0A0MT54

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000125

AC:

AN:

239124

AF XY:

0.00000760

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000293

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000188

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000754

AC:

AN:

1459368

Hom.:

Cov.:

AF XY:

0.00000964

AC XY:

AN XY:

725974

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33468

American (AMR)

AF:

0.0000224

AC:

AN:

44628

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26094

East Asian (EAS)

AF:

0.00

AC:

AN:

39658

South Asian (SAS)

AF:

0.00

AC:

AN:

86110

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51872

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5660

European-Non Finnish (NFE)

AF:

0.00000900

AC:

AN:

1111630

Other (OTH)

AF:

0.00

AC:

AN:

60248

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000197

AC:

AN:

152210

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41480

American (AMR)

AF:

0.00

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5170

South Asian (SAS)

AF:

0.00

AC:

AN:

4836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000441

AC:

AN:

68018

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000282

Hom.:

Bravo

AF:

0.00000378

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

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

Benign:1

Sep 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Inborn genetic diseases

Benign:1

May 08, 2025

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

-0.14

PromoterAI

0.078

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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