rs2272668

chr8-75551336-T-C

Variant summary

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

The NM_004133.5(HNF4G):c.383-52T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,014,188 control chromosomes in the GnomAD database, including 25,317 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 0.22 (3933 hom., cov: 31)
  • Exomes 𝑓: 0.22 (21384 hom.)
• Consequence: HNF4G NM_004133.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

HNF4G (HGNC:5026): (hepatocyte nuclear factor 4 gamma) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in several cellular components, including intercellular bridge; mitotic spindle; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF4G	NM_004133.5	c.383-52T>C		intron_variant		ENST00000396423.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF4G	ENST00000396423.4	c.383-52T>C		intron_variant		1	NM_004133.5
HNF4G	ENST00000354370.5	c.242-52T>C		intron_variant		1		P1
HNF4G	ENST00000674002.1	c.353-52T>C		intron_variant
HNF4G	ENST00000396419.5	n.239-52T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33826 AN: 151750 Hom.: 3936 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.215 AC: 185788 AN: 862318 Hom.: 21384 Cov.: 11 AF XY: 0.212 AC XY: 95482 AN XY: 450144

Gnomad4 AFR exome AF: 0.225

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.117

Gnomad4 SAS exome AF: 0.124

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.223 AC: 33837 AN: 151870 Hom.: 3933 Cov.: 31 AF XY: 0.225 AC XY: 16661 AN XY: 74206

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0962

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.226

Alfa AF: 0.220 Hom.: 4714

Bravo AF: 0.213

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.1
Dann	Benign	0.34

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: rs2272668; hg19: chr8-76463571;