Genetic Variant FOXF2:p.Gly306dup (chr6-1390850-G-GGGC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001452.2(FOXF2):c.917_919dupGCG(p.Gly306dup) variant causes a disruptive 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 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

2 publications found

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:

LINC01394 (HGNC:50670): (long intergenic non-protein coding RNA 1394)

LINC01394 links:

FOXF2-DT (HGNC:50662): (FOXF2 divergent transcript)

FOXF2-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FOXF2	NM_001452.2 link	c.917_919dupGCG	p.Gly306dup	disruptive_inframe_insertion	Exon 1 of 2	ENST00000645481.2	NP_001443.1	Q12947
FOXF2-DT	NR_189294.1 link	n.68+139_68+141dupGCC		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1 link	n.68+139_68+141dupGCC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	ENST00000645481.2 link	c.917_919dupGCG	p.Gly306dup	disruptive_inframe_insertion	Exon 1 of 2	NM_001452.2	ENSP00000496415.1	Q12947
LINC01394	ENST00000721686.1 link	n.89+139_89+141dupGCC		intron_variant	Intron 1 of 2
LINC01394	ENST00000721687.1 link	n.68+139_68+141dupGCC		intron_variant	Intron 1 of 3

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

GnomAD2 exomes

AF:

0.499

AC:

18078

AN:

36238

AF XY:

0.502

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 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

African (AFR)

AF:

0.668

AC:

16732

AN:

25040

American (AMR)

AF:

0.517

AC:

9586

AN:

18548

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

11035

AN:

19142

East Asian (EAS)

AF:

0.936

AC:

27339

AN:

29210

South Asian (SAS)

AF:

0.706

AC:

41077

AN:

58156

European-Finnish (FIN)

AF:

0.440

AC:

13868

AN:

31528

Middle Eastern (MID)

AF:

0.669

AC:

2562

AN:

3828

European-Non Finnish (NFE)

AF:

0.482

AC:

495763

AN:

1027746

Other (OTH)

AF:

0.555

AC:

29098

AN:

52454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

17868

35736

53604

71472

89340

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15430

30860

46290

61720

77150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.567

AC:

85868

AN:

151400

Hom.:

25117

Cov.:

AF XY:

0.568

AC XY:

42010

AN XY:

74010

show subpopulations

African (AFR)

AF:

0.654

AC:

26972

AN:

41270

American (AMR)

AF:

0.541

AC:

8253

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

2069

AN:

3460

East Asian (EAS)

AF:

0.926

AC:

4704

AN:

5078

South Asian (SAS)

AF:

0.745

AC:

3581

AN:

4806

European-Finnish (FIN)

AF:

0.437

AC:

4603

AN:

10532

Middle Eastern (MID)

AF:

0.668

AC:

191

AN:

286

European-Non Finnish (NFE)

AF:

0.498

AC:

33726

AN:

67712

Other (OTH)

AF:

0.598

AC:

1261

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1878

3756

5634

7512

9390

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.332

Hom.:

591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.082

Mutation Taster

=87/13

polymorphism (auto)

(source)

Splicing

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

Publications

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6-1390850-GGGCGGC-GGGCGGCGGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over