rs6103716

Positions:

• chr20-44370990-A-C
• chr20-44370990-A-G
• chr20-44370990-A-T

Variant summary

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

The NM_175914.5(HNF4A):​c.49+15137A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,058 control chromosomes in the GnomAD database, including 11,075 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 0.37 (11075 hom., cov: 33)
• Consequence: HNF4A NM_175914.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

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]

HNF4A-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNF4A	NM_175914.5	c.49+15137A>C		intron_variant		ENST00000316673.9	NP_787110.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNF4A	ENST00000316673.9	c.49+15137A>C		intron_variant		1	NM_175914.5	ENSP00000315180.4
HNF4A	ENST00000457232.5	c.49+15137A>C		intron_variant		1		ENSP00000396216.1
HNF4A	ENST00000609795.5	c.49+15137A>C		intron_variant		1		ENSP00000476609.1
HNF4A	ENST00000609262.5	c.-183+15137A>C		intron_variant		1		ENSP00000476310.1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56946 AN: 151940 Hom.: 11050 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.375 AC: 57014 AN: 152058 Hom.: 11075 Cov.: 33 AF XY: 0.382 AC XY: 28399 AN XY: 74322

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.385

Alfa AF: 0.347 Hom.: 5714

Bravo AF: 0.386

Asia WGS AF: 0.483 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6103716; hg19: chr20-42999630;