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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Links

HNF1B (HGNC:11630):

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 linkuse as main transcript	c.545-2704G>C		intron_variant		ENST00000617811.5

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
HNF1B	ENST00000617811.5 linkuse as main transcript	c.545-2704G>C	intron_variant	1	NM_000458.4		P35680-1
HNF1B	ENST00000613727.4 linkuse as main transcript	c.545-2782G>C	intron_variant	1
HNF1B	ENST00000621123.4 linkuse as main transcript	c.545-2782G>C	intron_variant	1		P1	P35680-2
HNF1B	ENST00000614313.4 linkuse as main transcript	c.545-2704G>C	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0178

AC:

2706

AN:

151936

Hom.:

Cov.:

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

Alfa

AF:

0.000533

Hom.:

15577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Cadd

Benign

0.042

Splicing

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.