Variant chr11-32388079-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024426.6(WT1):c.*978_*979insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 236,018 control chromosomes in the GnomAD database, including 5,177 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 2695 hom., cov: 30)

Exomes 𝑓: 0.19 ( 2482 hom. )

Consequence

WT1
NM_024426.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:3

Conservation

PhyloP100: 0.165

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-32388079-A-AT is Benign according to our data. Variant chr11-32388079-A-AT is described in ClinVar as [Benign]. Clinvar id is 304383.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WT1	NM_024426.6 linkuse as main transcript	c.978_979insA		3_prime_UTR_variant	10/10	ENST00000452863.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WT1	ENST00000452863.10 linkuse as main transcript	c.978_979insA		3_prime_UTR_variant	10/10	1	NM_024426.6		P19544-7

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22387

AN:

151496

Hom.:

2681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0619

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.153

GnomAD4 exome

AF:

0.187

AC:

15817

AN:

84404

Hom.:

2482

Cov.:

AF XY:

0.182

AC XY:

7121

AN XY:

39076

show subpopulations

Gnomad4 AFR exome

AF:

0.0602

Gnomad4 AMR exome

AF:

0.306

Gnomad4 ASJ exome

AF:

0.135

Gnomad4 EAS exome

AF:

0.556

Gnomad4 SAS exome

AF:

0.302

Gnomad4 FIN exome

AF:

0.117

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.151

GnomAD4 genome

AF:

0.148

AC:

22409

AN:

151614

Hom.:

2695

Cov.:

AF XY:

0.159

AC XY:

11805

AN XY:

74088

show subpopulations

Gnomad4 AFR

AF:

0.0618

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.657

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.0640

Hom.:

Asia WGS

AF:

0.436

AC:

1514

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Nephroblastoma

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Meacham syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Nephrotic syndrome, type 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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