GeneBe

rs58549495

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024426.6(WT1):​c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

WT1
NM_024426.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

2 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: Labcorp Genetics (formerly Invitae), ClinGen, G2P
  • familial idiopathic steroid-resistant nephrotic syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Frasier syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024426.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
WT1
NM_024426.6
MANE Select
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 10 of 10NP_077744.4
WT1
NM_024424.5
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 10 of 10NP_077742.3H0Y7K5
WT1
NM_001407044.1
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 10 of 10NP_001393973.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
WT1
ENST00000452863.10
TSL:1 MANE Select
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 10 of 10ENSP00000415516.5P19544-7
WT1
ENST00000639563.4
TSL:1
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 9 of 9ENSP00000492269.3P19544-8
WT1
ENST00000332351.9
TSL:1
c.*1035_*1054delGTGTGTGTGTGTGTGTGTGT
3_prime_UTR
Exon 9 of 9ENSP00000331327.5J3KNN9

Frequencies

GnomAD3 genomes
AF:
0.0000137
AC:
2
AN:
146470
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000499
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
82622
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
38146
African (AFR)
AF:
0.00
AC:
0
AN:
3892
American (AMR)
AF:
0.00
AC:
0
AN:
2512
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
5124
East Asian (EAS)
AF:
0.00
AC:
0
AN:
11494
South Asian (SAS)
AF:
0.00
AC:
0
AN:
696
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
752
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
492
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
50852
Other (OTH)
AF:
0.00
AC:
0
AN:
6808
GnomAD4 genome
AF:
0.0000137
AC:
2
AN:
146470
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
71174
show subpopulations
African (AFR)
AF:
0.0000499
AC:
2
AN:
40112
American (AMR)
AF:
0.00
AC:
0
AN:
14694
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3390
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4984
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4568
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9592
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
65926
Other (OTH)
AF:
0.00
AC:
0
AN:
2008
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
53

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs58549495; hg19: chr11-32409549; API