rs757210
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000458(HNF1B):c.545-2704G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 151936 control chromosomes in the gnomAD Genomes database, including 43 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 0.018 ( 43 hom., cov: 31)
Consequence
HNF1B
NM_000458 intron
NM_000458 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.71
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (Cadd=0.042).
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.0178 (2706/151936) while in subpopulation NFE AF= 0.0241 (1638/67990). AF 95% confidence interval is 0.0231. There are 43 homozygotes in gnomad. There are 1330 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2706 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF1B | NM_000458.4 | c.545-2704G>C | intron_variant | ENST00000617811.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF1B | ENST00000617811.5 | c.545-2704G>C | intron_variant | 1 | NM_000458.4 | ||||
HNF1B | ENST00000613727.4 | c.545-2782G>C | intron_variant | 1 | |||||
HNF1B | ENST00000621123.4 | c.545-2782G>C | intron_variant | 1 | P1 | ||||
HNF1B | ENST00000614313.4 | c.545-2704G>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0178 AC: 2706AN: 151936Hom.: 43 Cov.: 31
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
Cadd
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at