Menu
GeneBe

rs757210

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_000458.4(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 152,054 control chromosomes in the GnomAD 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_000458.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (Cadd=0.047).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0178 (2706/152054) while in subpopulation NFE AF= 0.0241 (1638/67982). AF 95% confidence interval is 0.0231. There are 43 homozygotes in gnomad4. There are 1331 alleles in male gnomad4 subpopulation. 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
HNF1BNM_000458.4 linkuse as main transcriptc.545-2704G>C intron_variant ENST00000617811.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HNF1BENST00000617811.5 linkuse as main transcriptc.545-2704G>C intron_variant 1 NM_000458.4 P35680-1
HNF1BENST00000613727.4 linkuse as main transcriptc.545-2782G>C intron_variant 1
HNF1BENST00000621123.4 linkuse as main transcriptc.545-2782G>C intron_variant 1 P1P35680-2
HNF1BENST00000614313.4 linkuse as main transcriptc.545-2704G>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0178
AC:
2706
AN:
151936
Hom.:
43
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00462
Gnomad AMI
AF:
0.00330
Gnomad AMR
AF:
0.0164
Gnomad ASJ
AF:
0.0297
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0232
Gnomad FIN
AF:
0.0345
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0241
Gnomad OTH
AF:
0.0173
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0178
AC:
2706
AN:
152054
Hom.:
43
Cov.:
31
AF XY:
0.0179
AC XY:
1331
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.00461
Gnomad4 AMR
AF:
0.0164
Gnomad4 ASJ
AF:
0.0297
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0232
Gnomad4 FIN
AF:
0.0345
Gnomad4 NFE
AF:
0.0241
Gnomad4 OTH
AF:
0.0171
Alfa
AF:
0.000533
Hom.:
15577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Cadd
Benign
0.047

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs757210; hg19: -; API