rs11649743
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000458.4(HNF1B):c.1046-4308T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 151,976 control chromosomes in the GnomAD database, including 54,459 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.84 ( 54459 hom., cov: 29)
Consequence
HNF1B
NM_000458.4 intron
NM_000458.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.75
Genes affected
HNF1B (HGNC:11630): (HNF1 homeobox B) This gene encodes a member of the homeodomain-containing superfamily of transcription factors. The protein binds to DNA as either a homodimer, or a heterodimer with the related protein hepatocyte nuclear factor 1-alpha. The gene has been shown to function in nephron development, and regulates development of the embryonic pancreas. Mutations in this gene result in renal cysts and diabetes syndrome and noninsulin-dependent diabetes mellitus, and expression of this gene is altered in some types of cancer. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF1B | NM_000458.4 | c.1046-4308T>C | intron_variant | ENST00000617811.5 | |||
LOC105371754 | XR_001752876.2 | n.684+344A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF1B | ENST00000617811.5 | c.1046-4308T>C | intron_variant | 1 | NM_000458.4 | ||||
HNF1B | ENST00000613727.4 | c.968-4308T>C | intron_variant | 1 | |||||
HNF1B | ENST00000621123.4 | c.968-4308T>C | intron_variant | 1 | P1 | ||||
HNF1B | ENST00000614313.4 | c.1046-4308T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.844 AC: 128204AN: 151858Hom.: 54420 Cov.: 29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.844 AC: 128301AN: 151976Hom.: 54459 Cov.: 29 AF XY: 0.844 AC XY: 62706AN XY: 74306
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at