Variant 8-75538863-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001330561.2(HNF4G):c.-23-4948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,964 control chromosomes in the GnomAD database, including 29,339 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 0.60 ( 29339 hom., cov: 32)

Consequence

HNF4G
NM_001330561.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.123

Variant links:

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]

HNF4G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
HNF4G	NM_001330561.2 link	c.-23-4948A>G	intron_variant	NP_001317490.1	Q14541-1
HNF4G	XM_017013373.2 link	c.-23-4948A>G	intron_variant	XP_016868862.1	Q14541-1
HNF4G	XM_017013374.2 link	c.-23-4948A>G	intron_variant	XP_016868863.1	Q14541-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNF4G	ENST00000354370.5 link	c.-23-4948A>G		intron_variant		1		ENSP00000346339.1		Q14541-1
HNF4G	ENST00000396419.5 link	n.144-8724A>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.604

AC:

91721

AN:

151842

Hom.:

29308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.820

Gnomad AMI

AF:

0.594

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.582

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

GnomAD4 genome

AF:

0.604

AC:

91806

AN:

151964

Hom.:

29339

Cov.:

AF XY:

0.604

AC XY:

44858

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.820

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.508

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.473

Gnomad4 FIN

AF:

0.663

Gnomad4 NFE

AF:

0.524

Gnomad4 OTH

AF:

0.582

Alfa

AF:

0.519

Hom.:

29712

Bravo

AF:

0.598

Asia WGS

AF:

0.480

AC:

1670

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.2

DANN

Benign

0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over