chr17-37744659-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP3BP4_ModerateBP6BS1BS2
The NM_000458.4(HNF1B):c.226G>T(p.Gly76Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000399 in 1,613,178 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000458.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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HNF1B | ENST00000617811.5 | c.226G>T | p.Gly76Cys | missense_variant | Exon 1 of 9 | 1 | NM_000458.4 | ENSP00000480291.1 | ||
HNF1B | ENST00000621123.4 | c.226G>T | p.Gly76Cys | missense_variant | Exon 1 of 9 | 1 | ENSP00000482711.1 | |||
HNF1B | ENST00000613727.4 | c.226G>T | p.Gly76Cys | missense_variant | Exon 1 of 7 | 1 | ENSP00000477524.1 | |||
HNF1B | ENST00000614313.4 | c.226G>T | p.Gly76Cys | missense_variant | Exon 1 of 8 | 5 | ENSP00000482529.1 |
Frequencies
GnomAD3 genomes AF: 0.000617 AC: 94AN: 152252Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000575 AC: 144AN: 250430Hom.: 1 AF XY: 0.000634 AC XY: 86AN XY: 135656
GnomAD4 exome AF: 0.000375 AC: 548AN: 1460808Hom.: 2 Cov.: 35 AF XY: 0.000359 AC XY: 261AN XY: 726774
GnomAD4 genome AF: 0.000623 AC: 95AN: 152370Hom.: 1 Cov.: 33 AF XY: 0.000698 AC XY: 52AN XY: 74516
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:3
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Identified in multiple patients with structural renal abnormalities, however, family segregation studies have been limited, functional studies have not been performed, and only the HNF1B gene was sequenced in most publications (Ulinski et al., 2006; Nakayama et al., 2010; Musetti et al., 2014, Raaijmakers et al., 2015; Okorn et al., 2019); Identified in an individual with maturity-onset diabetes of the young, however, additional clinical and segregation information was not provided (Bellanne-Chatelot et al., 2005); Identified in randomly selected individuals from the Framingham and Jackson Heart Studies (Flannick et al., 2013); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21775974, 24097065, 24387224, 20155289, 26764160, 25500806, 16249435, 30666461, 16371430, 31365591, 34426522, 33324081) -
BS1, PP3 -
Renal cysts and diabetes syndrome Uncertain:2Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
This variant is interpreted as a Uncertain Significance - Conflicting Evidence, for Renal cysts and diabetes syndrome, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder (PMID:23539225). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. -
not specified Benign:3
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HNF1B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Nonpapillary renal cell carcinoma Benign:1
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Congenital anomaly of kidney and urinary tract Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at