rs7501939

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The NM_000458(HNF1B):c.345-1526G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. 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: not found (cov: 33)

Consequence

HNF1B
NM_000458 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Links

HNF1B (HGNC:11630):

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 33.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF1B	NM_000458.4 linkuse as main transcript	c.345-1526G>C		intron_variant		ENST00000617811.5

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
HNF1B	ENST00000617811.5 linkuse as main transcript	c.345-1526G>C	intron_variant	1	NM_000458.4		P35680-1
HNF1B	ENST00000613727.4 linkuse as main transcript	c.345-1526G>C	intron_variant	1
HNF1B	ENST00000621123.4 linkuse as main transcript	c.345-1526G>C	intron_variant	1		P1	P35680-2
HNF1B	ENST00000614313.4 linkuse as main transcript	c.345-1526G>C	intron_variant	5

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd