dbSNP rs2255531: HNF1A-AS1:n.135-191C>T (chr12-120977112-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000433033.3(HNF1A-AS1):n.135-191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,942 control chromosomes in the GnomAD database, including 9,911 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 0.36 ( 9911 hom., cov: 32)

Consequence

HNF1A-AS1
ENST00000433033.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.363

Variant links:

Genes affected

HNF1A-AS1 (HGNC:26785): (HNF1A antisense RNA 1)

HNF1A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HNF1A-AS1	ENST00000433033.3 link	n.135-191C>T	intron_variant	Intron 1 of 3	3
HNF1A-AS1	ENST00000535301.2 link	n.323-2514C>T	intron_variant	Intron 1 of 1	4
HNF1A-AS1	ENST00000537361.1 link	n.263+3532C>T	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54231

AN:

151824

Hom.:

9911

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.537

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.369

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

GnomAD4 genome

AF:

0.357

AC:

54253

AN:

151942

Hom.:

9911

Cov.:

AF XY:

0.365

AC XY:

27108

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.411

Gnomad4 SAS

AF:

0.473

Gnomad4 FIN

AF:

0.418

Gnomad4 NFE

AF:

0.361

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.360

Hom.:

2097

Bravo

AF:

0.349

Asia WGS

AF:

0.454

AC:

1575

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over