Genetic Variant HNF1A-AS1:n.295+13237A>G (chr12-120967407-T-C) – 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+13237A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,928 control chromosomes in the GnomAD database, including 14,464 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 0.43 ( 14464 hom., cov: 31)

Consequence

HNF1A-AS1
ENST00000619441.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

16 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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+13237A>G	intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000646404.1 link	n.302-1492A>G	intron_variant	Intron 2 of 2
HNF1A-AS1	ENST00000647473.1 link	n.598+2891A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65662

AN:

151810

Hom.:

14446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.414

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.413

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

GnomAD4 genome

AF:

0.433

AC:

65715

AN:

151928

Hom.:

14464

Cov.:

AF XY:

0.426

AC XY:

31621

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.414

AC:

17157

AN:

41450

American (AMR)

AF:

0.294

AC:

4490

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1330

AN:

3468

East Asian (EAS)

AF:

0.581

AC:

3007

AN:

5172

South Asian (SAS)

AF:

0.365

AC:

1758

AN:

4822

European-Finnish (FIN)

AF:

0.442

AC:

4642

AN:

10500

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.472

AC:

32080

AN:

67944

Other (OTH)

AF:

0.411

AC:

864

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1863

3726

5590

7453

9316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.444

Hom.:

27027

Bravo

AF:

0.421

Asia WGS

AF:

0.444

AC:

1544

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.078

(source)

DANN

Benign

0.42

PhyloP100

-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