rs2272668

Variant names:

• chr8-75551336-T-A
• rs2272668
• NM_004133.5:c.383-52T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-75551336-T-A
• chr8-75551336-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004133.5(HNF4G):​c.383-52T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000116 in 863,912 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000012 (0 hom.)
• Consequence: HNF4G NM_004133.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HNF4G	NM_004133.5	c.383-52T>A		intron_variant	Intron 3 of 9	ENST00000396423.4	NP_004124.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNF4G	ENST00000396423.4	c.383-52T>A		intron_variant	Intron 3 of 9	1	NM_004133.5	ENSP00000379701.3
HNF4G	ENST00000354370.5	c.242-52T>A		intron_variant	Intron 4 of 10	1		ENSP00000346339.1
HNF4G	ENST00000674002.1	c.353-52T>A		intron_variant	Intron 3 of 9			ENSP00000501146.1
HNF4G	ENST00000396419.5	n.239-52T>A		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000116 AC: 1 AN: 863912 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 450982

African (AFR) AF: 0.00 AC: 0 AN: 21190

American (AMR) AF: 0.00 AC: 0 AN: 38784

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21202

East Asian (EAS) AF: 0.0000275 AC: 1 AN: 36310

South Asian (SAS) AF: 0.00 AC: 0 AN: 68066

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51678

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4452

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 582032

Other (OTH) AF: 0.00 AC: 0 AN: 40198

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.8
DANN	Benign	0.33
PhyloP100		0.021

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

Other links and lift over

dbSNP: rs2272668; hg19: chr8-76463571;