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GeneBe

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

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
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
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.

Other links and lift over

dbSNP: rs757210; hg19: -;