17-37687305-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The ENST00000613727.4(HNF1B):c.1349G>A(p.Gly450Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000613727.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF1B | NM_000458.4 | c.*67G>A | 3_prime_UTR_variant | 9/9 | ENST00000617811.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF1B | ENST00000613727.4 | c.1349G>A | p.Gly450Asp | missense_variant | 7/7 | 1 | |||
HNF1B | ENST00000617811.5 | c.*67G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_000458.4 | |||
HNF1B | ENST00000621123.4 | c.*67G>A | 3_prime_UTR_variant | 9/9 | 1 | P1 | |||
HNF1B | ENST00000614313.4 | c.1622G>A | p.Gly541Asp | missense_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251064Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135702
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461606Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727100
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
HNF1B-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 08, 2024 | The HNF1B c.1349G>A variant is predicted to result in the amino acid substitution p.Gly450Asp. In the alternative transcript NM_001304286.1, this variant is defined as c.1349G>A (p.Gly450Asp). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at