rs1008284

chr17-37702453-A-G

Variant summary

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

The NM_000458.4(HNF1B):c.1340-1276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 151,998 control chromosomes in the GnomAD database, including 45,071 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 0.77 (45071 hom., cov: 30)
• Consequence: HNF1B NM_000458.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF1B	NM_000458.4	c.1340-1276T>C		intron_variant		ENST00000617811.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF1B	ENST00000617811.5	c.1340-1276T>C		intron_variant		1	NM_000458.4
HNF1B	ENST00000613727.4	c.1261+2464T>C		intron_variant		1
HNF1B	ENST00000621123.4	c.1262-1276T>C		intron_variant		1		P1
HNF1B	ENST00000614313.4	c.1340-1276T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116851 AN: 151880 Hom.: 45047 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.769 AC: 116917 AN: 151998 Hom.: 45071 Cov.: 30 AF XY: 0.767 AC XY: 56936 AN XY: 74270

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.758

Alfa AF: 0.767 Hom.: 9069

Bravo AF: 0.767

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008284; hg19: chr17-36062458;