Variant chr6-1390850-G-GGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001452.2(FOXF2):c.917_919dup(p.Gly306dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 1,417,052 control chromosomes in the GnomAD database, including 195,064 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 25117 hom., cov: 0)

Exomes 𝑓: 0.51 ( 169947 hom. )

Consequence

FOXF2
NM_001452.2 inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Variant links:

Genes affected

FOXF2 (HGNC:3810): (forkhead box F2) FOXF2 encodes forkhead box F2, one of many human homologues of the Drosophila melanogaster transcription factor forkhead. FOXF2 is expressed in lung and placenta, and has been shown to transcriptionally activate several lung-specific genes. [provided by RefSeq, Jul 2008]

FOXF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXF2	NM_001452.2 linkuse as main transcript	c.917_919dup	p.Gly306dup	inframe_insertion	1/2	ENST00000645481.2	NP_001443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 linkuse as main transcript	c.917_919dup	p.Gly306dup	inframe_insertion	1/2		NM_001452.2	ENSP00000496415	P1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

85816

AN:

151302

Hom.:

25110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.598

Gnomad EAS

AF:

0.926

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.593

GnomAD3 exomes

AF:

0.499

AC:

18078

AN:

36238

Hom.:

4714

AF XY:

0.502

AC XY:

10163

AN XY:

20250

show subpopulations

Gnomad AFR exome

AF:

0.599

Gnomad AMR exome

AF:

0.466

Gnomad ASJ exome

AF:

0.500

Gnomad EAS exome

AF:

0.888

Gnomad SAS exome

AF:

0.651

Gnomad FIN exome

AF:

0.385

Gnomad NFE exome

AF:

0.425

Gnomad OTH exome

AF:

0.488

GnomAD4 exome

AF:

0.511

AC:

647060

AN:

1265652

Hom.:

169947

Cov.:

AF XY:

0.516

AC XY:

319105

AN XY:

617968

show subpopulations

Gnomad4 AFR exome

AF:

0.668

Gnomad4 AMR exome

AF:

0.517

Gnomad4 ASJ exome

AF:

0.576

Gnomad4 EAS exome

AF:

0.936

Gnomad4 SAS exome

AF:

0.706

Gnomad4 FIN exome

AF:

0.440

Gnomad4 NFE exome

AF:

0.482

Gnomad4 OTH exome

AF:

0.555

GnomAD4 genome

AF:

0.567

AC:

85868

AN:

151400

Hom.:

25117

Cov.:

AF XY:

0.568

AC XY:

42010

AN XY:

74010

show subpopulations

Gnomad4 AFR

AF:

0.654

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.598

Gnomad4 EAS

AF:

0.926

Gnomad4 SAS

AF:

0.745

Gnomad4 FIN

AF:

0.437

Gnomad4 NFE

AF:

0.498

Gnomad4 OTH

AF:

0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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