rs121918673
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PP3_StrongPP5BS2
The ENST00000617811.5(HNF1B):c.1395C>G(p.Ser465Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,552,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000617811.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNF1B | NM_000458.4 | c.1395C>G | p.Ser465Arg | missense_variant | 7/9 | ENST00000617811.5 | NP_000449.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF1B | ENST00000617811.5 | c.1395C>G | p.Ser465Arg | missense_variant | 7/9 | 1 | NM_000458.4 | ENSP00000480291 | ||
HNF1B | ENST00000621123.4 | c.1317C>G | p.Ser439Arg | missense_variant | 7/9 | 1 | ENSP00000482711 | P1 | ||
HNF1B | ENST00000613727.4 | c.1261+3795C>G | intron_variant | 1 | ENSP00000477524 | |||||
HNF1B | ENST00000614313.4 | c.1395C>G | p.Ser465Arg | missense_variant | 7/8 | 5 | ENSP00000482529 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000189 AC: 3AN: 159042Hom.: 0 AF XY: 0.0000239 AC XY: 2AN XY: 83694
GnomAD4 exome AF: 0.00000357 AC: 5AN: 1400062Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 690700
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
Renal cysts and diabetes syndrome Pathogenic:1Uncertain:1
Pathogenic, criteria provided, single submitter | literature only | Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg | Jul 06, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Type 2 diabetes mellitus Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2002 | - - |
Ovarian cancer Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Molecular Epidemiology of Birth Defects, West China Second University Hospital, Sichuan University | Jan 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at