Genetic Variant HNF1A-AS1:n.295+15515G>A (chr12-120965129-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000619441.2(HNF1A-AS1):n.295+15515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,930 control chromosomes in the GnomAD database, including 6,799 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 0.28 ( 6799 hom., cov: 31)

Consequence

HNF1A-AS1
ENST00000619441.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0670

Publications

63 publications found

Variant links:

Genes affected

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

HNF1A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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	ENST00000619441.2 link	n.295+15515G>A	intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000647473.1 link	n.599-1785G>A	intron_variant	Intron 4 of 4
HNF1A-AS1	ENST00000760046.1 link	n.410+9356G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

42948

AN:

151812

Hom.:

6777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.270

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

GnomAD4 genome

AF:

0.283

AC:

43010

AN:

151930

Hom.:

6799

Cov.:

AF XY:

0.280

AC XY:

20752

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.400

AC:

16560

AN:

41378

American (AMR)

AF:

0.184

AC:

2808

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

879

AN:

3470

East Asian (EAS)

AF:

0.533

AC:

2740

AN:

5144

South Asian (SAS)

AF:

0.273

AC:

1318

AN:

4822

European-Finnish (FIN)

AF:

0.207

AC:

2191

AN:

10560

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15739

AN:

67966

Other (OTH)

AF:

0.269

AC:

569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1465

2930

4395

5860

7325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.249

Hom.:

22486

Bravo

AF:

0.288

Asia WGS

AF:

0.392

AC:

1363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.3

(source)

DANN

Benign

0.60

PhyloP100

-0.067

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over