rs1183910

Positions:

• chr12-120983004-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000545.8(HNF1A):​c.326+3910G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,090 control chromosomes in the GnomAD database, including 6,826 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 (6826 hom., cov: 32)
• Consequence: HNF1A NM_000545.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF1A	NM_000545.8	c.326+3910G>A		intron_variant		ENST00000257555.11
HNF1A	NM_001306179.2	c.326+3910G>A		intron_variant
HNF1A	NM_001406915.1	c.326+3910G>A		intron_variant
HNF1A	XM_024449168.2	c.326+3910G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF1A	ENST00000257555.11	c.326+3910G>A		intron_variant		1	NM_000545.8	P4

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42840 AN: 151972 Hom.: 6824 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.282 AC: 42846 AN: 152090 Hom.: 6826 Cov.: 32 AF XY: 0.291 AC XY: 21633 AN XY: 74348

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.312

Alfa AF: 0.323 Hom.: 11259

Bravo AF: 0.269

Asia WGS AF: 0.388 AC: 1346 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	0.0020
DANN	Benign	0.68

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

LitVar

Other links and lift over

dbSNP: rs1183910; hg19: chr12-121420807;