rs3746575

chr20-44429456-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_175914.5(HNF4A):c.1217-67C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 1,595,626 control chromosomes in the GnomAD database, including 279,916 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.57 (24593 hom., cov: 28)
  • Exomes 𝑓: 0.59 (255323 hom.)
• Consequence: HNF4A NM_175914.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.378

Genes affected

HNF4A (HGNC:5024): (hepatocyte nuclear factor 4 alpha) The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 20-44429456-C-G is Benign according to our data. Variant chr20-44429456-C-G is described in ClinVar as [Benign]. Clinvar id is 676886.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-44429456-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF4A	NM_175914.5	c.1217-67C>G		intron_variant		ENST00000316673.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF4A	ENST00000316673.9	c.1217-67C>G		intron_variant		1	NM_175914.5

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85607 AN: 151020 Hom.: 24597 Cov.: 28

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.591 AC: 853730 AN: 1444488 Hom.: 255323 AF XY: 0.593 AC XY: 426397 AN XY: 719238

Gnomad4 AFR exome AF: 0.529

Gnomad4 AMR exome AF: 0.429

Gnomad4 ASJ exome AF: 0.702

Gnomad4 EAS exome AF: 0.382

Gnomad4 SAS exome AF: 0.602

Gnomad4 FIN exome AF: 0.597

Gnomad4 NFE exome AF: 0.603

Gnomad4 OTH exome AF: 0.586

GnomAD4 genome AF: 0.567 AC: 85635 AN: 151138 Hom.: 24593 Cov.: 28 AF XY: 0.563 AC XY: 41530 AN XY: 73760

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.585

Alfa AF: 0.583 Hom.: 3276

Bravo AF: 0.558

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Maturity onset diabetes mellitus in young Benign:1

Benign, criteria provided, single submitter

research

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

-

Potent mutations in HNF4A are associated with poor insulin secretion in response to hyperglycemia. Associated with MODY1. Patients initially respond well to sulfonylureas but eventually become insulin dependent. However, more evidence is required to ascertain the role of this particular variant rs3746575 in MODY, yet. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.48
Dann	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3746575; hg19: chr20-43058096; COSMIC: COSV57380799; COSMIC: COSV57380799;