17-37727883-G-C

Position:

• chr17-37727883-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000458.4(HNF1B):​c.1045+3712C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,114 control chromosomes in the GnomAD database, including 1,438 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 0.12 (1438 hom., cov: 31)
• Consequence: HNF1B NM_000458.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNF1B	NM_000458.4	c.1045+3712C>G		intron_variant		ENST00000617811.5	NP_000449.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNF1B	ENST00000617811.5	c.1045+3712C>G		intron_variant		1	NM_000458.4	ENSP00000480291
HNF1B	ENST00000613727.4	c.967+3712C>G		intron_variant		1		ENSP00000477524
HNF1B	ENST00000621123.4	c.967+3712C>G		intron_variant		1		ENSP00000482711	P1
HNF1B	ENST00000614313.4	c.1045+3712C>G		intron_variant		5		ENSP00000482529

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18739 AN: 151996 Hom.: 1439 Cov.: 31

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.136

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18730 AN: 152114 Hom.: 1438 Cov.: 31 AF XY: 0.125 AC XY: 9330 AN XY: 74354

Gnomad4 AFR AF: 0.0424

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0462 Hom.: 54

Bravo AF: 0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs3786127; hg19: chr17-36087874;