Genetic Variant FOXF2:p.Ala40_Ala41del (chr6-1390041-CCCGCCG-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001452.2(FOXF2):c.118_123delGCCGCC(p.Ala40_Ala41del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,352,428 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0023 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0013 ( 2 hom. )

Consequence

FOXF2
NM_001452.2 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.08

Publications

0 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 332 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001452.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FOXF2	NM_001452.2	MANE Select	c.118_123delGCCGCC	p.Ala40_Ala41del	conservative_inframe_deletion	Exon 1 of 2	NP_001443.1	Q12947
FOXF2-DT	NR_189293.1		n.458+35_458+40delCGGCGG		intron	N/A
FOXF2-DT	NR_189294.1		n.69-821_69-816delCGGCGG		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FOXF2	ENST00000645481.2	MANE Select	c.118_123delGCCGCC	p.Ala40_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENSP00000496415.1	Q12947
LINC01394	ENST00000721686.1		n.89+945_89+950delCGGCGG		intron	N/A
LINC01394	ENST00000721687.1		n.69-821_69-816delCGGCGG		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00229

AC:

332

AN:

145192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00551

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000204

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000825

Gnomad SAS

AF:

0.00192

Gnomad FIN

AF:

0.00140

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00120

Gnomad OTH

AF:

0.00199

GnomAD2 exomes

AF:

0.00194

AC:

AN:

34036

AF XY:

0.00218

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000610

Gnomad ASJ exome

AF:

0.000346

Gnomad EAS exome

AF:

0.00221

Gnomad FIN exome

AF:

0.000753

Gnomad NFE exome

AF:

0.00301

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00126

AC:

1515

AN:

1207138

Hom.:

AF XY:

0.00129

AC XY:

762

AN XY:

592582

show subpopulations

African (AFR)

AF:

0.00567

AC:

138

AN:

24322

American (AMR)

AF:

0.000652

AC:

AN:

21476

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19220

East Asian (EAS)

AF:

0.000695

AC:

AN:

23032

South Asian (SAS)

AF:

0.00170

AC:

AN:

58384

European-Finnish (FIN)

AF:

0.000748

AC:

AN:

28078

Middle Eastern (MID)

AF:

0.00146

AC:

AN:

3418

European-Non Finnish (NFE)

AF:

0.00117

AC:

1148

AN:

981040

Other (OTH)

AF:

0.00154

AC:

AN:

48168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

117

176

234

293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

150

200

250

<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:

0.00229

AC:

332

AN:

145290

Hom.:

Cov.:

AF XY:

0.00215

AC XY:

152

AN XY:

70760

show subpopulations

African (AFR)

AF:

0.00552

AC:

222

AN:

40200

American (AMR)

AF:

0.000204

AC:

AN:

14708

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3392

East Asian (EAS)

AF:

0.000828

AC:

AN:

4832

South Asian (SAS)

AF:

0.00171

AC:

AN:

4692

European-Finnish (FIN)

AF:

0.00140

AC:

AN:

8546

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00120

AC:

AN:

65728

Other (OTH)

AF:

0.00197

AC:

AN:

2026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000558

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.1

Mutation Taster

=188/12

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCGCCG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over