NM_000545.8:c.1460G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000545.8(HNF1A):c.1460G>A(p.Ser487Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,612,298 control chromosomes in the GnomAD database, including 80,461 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S487G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.27 ( 6416 hom., cov: 32)

Exomes 𝑓: 0.31 ( 74045 hom. )

Consequence

HNF1A
NM_000545.8 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:15O:1

Conservation

PhyloP100: 1.05

Publications

159 publications found

Variant links:

Genes affected

HNF1A (HGNC:11621): (HNF1 homeobox A) The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

HNF1A Gene-Disease associations (from GenCC):

monogenic diabetes
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
type 1 diabetes mellitus 20
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Genomics England PanelApp
diabetes mellitus, noninsulin-dependent
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
maturity-onset diabetes of the young type 3
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
hyperinsulinism due to HNF1A deficiency
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
maturity-onset diabetes of the young
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
nonpapillary renal cell carcinoma
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

HNF1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001606971).

BP6

Variant 12-120997624-G-A is Benign according to our data. Variant chr12-120997624-G-A is described in ClinVar as Benign. ClinVar VariationId is 129230.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000545.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
HNF1A	NM_000545.8	MANE Select	c.1460G>A	p.Ser487Asn	missense	Exon 7 of 10	NP_000536.6
HNF1A	NM_001306179.2		c.1460G>A	p.Ser487Asn	missense	Exon 7 of 10	NP_001293108.2
HNF1A	NM_001406915.1		c.1309+882G>A		intron	N/A	NP_001393844.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
HNF1A	ENST00000257555.11	TSL:1 MANE Select	c.1460G>A	p.Ser487Asn	missense	Exon 7 of 10	ENSP00000257555.5
HNF1A	ENST00000544413.2	TSL:1	c.1460G>A	p.Ser487Asn	missense	Exon 7 of 10	ENSP00000438804.1
HNF1A	ENST00000535955.5	TSL:1	n.176G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41508

AN:

152026

Hom.:

6414

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.487

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.305

GnomAD2 exomes

AF:

0.337

AC:

83546

AN:

247590

AF XY:

0.343

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.371

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.312

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.312

AC:

456021

AN:

1460154

Hom.:

74045

Cov.:

AF XY:

0.316

AC XY:

229707

AN XY:

726350

show subpopulations

African (AFR)

AF:

0.121

AC:

4034

AN:

33468

American (AMR)

AF:

0.373

AC:

16586

AN:

44508

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

12235

AN:

26106

East Asian (EAS)

AF:

0.523

AC:

20716

AN:

39606

South Asian (SAS)

AF:

0.411

AC:

35356

AN:

86098

European-Finnish (FIN)

AF:

0.309

AC:

16395

AN:

53086

Middle Eastern (MID)

AF:

0.484

AC:

2789

AN:

5766

European-Non Finnish (NFE)

AF:

0.295

AC:

328233

AN:

1111166

Other (OTH)

AF:

0.326

AC:

19677

AN:

60350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

18777

37554

56332

75109

93886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10956

21912

32868

43824

54780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.273

AC:

41510

AN:

152144

Hom.:

6416

Cov.:

AF XY:

0.280

AC XY:

20838

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.128

AC:

5314

AN:

41534

American (AMR)

AF:

0.345

AC:

5265

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1594

AN:

3470

East Asian (EAS)

AF:

0.486

AC:

2516

AN:

5172

South Asian (SAS)

AF:

0.403

AC:

1945

AN:

4822

European-Finnish (FIN)

AF:

0.321

AC:

3402

AN:

10584

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.299

AC:

20345

AN:

67974

Other (OTH)

AF:

0.312

AC:

657

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1482

2964

4446

5928

7410

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.302

Hom.:

26154

Bravo

AF:

0.267

TwinsUK

AF:

0.294

AC:

1090

ALSPAC

AF:

0.300

AC:

1156

ESP6500AA

AF:

0.123

AC:

541

ESP6500EA

AF:

0.311

AC:

2676

ExAC

AF:

0.331

AC:

40202

Asia WGS

AF:

0.419

AC:

1452

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (7)

Maturity-onset diabetes of the young type 3 (3)

not provided (3)

Maturity onset diabetes mellitus in young (1)

Nonpapillary renal cell carcinoma (1)

Type 2 diabetes mellitus (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.21

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.46

Eigen

Benign

-0.22

Eigen_PC

Benign

-0.10

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.52

MetaRNN

Benign

0.0016

MetaSVM

Benign

-1.1

PhyloP100

1.1

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.61

REVEL

Uncertain

0.35

Sift

Benign

0.11

Sift4G

Benign

0.27

Polyphen

0.0

Vest4

0.13

MPC

0.12

ClinPred

0.0043

GERP RS

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.75

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over