Variant 6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_001452.2(FOXF2):c.115_123delGCCGCCGCC(p.Ala39_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 0.000794 in 1,354,610 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 31)

Exomes 𝑓: 0.00069 ( 1 hom. )

Consequence

FOXF2
NM_001452.2 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.31

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:

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

FOXF2-DT links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 6-1390041-CCCGCCGCCG-C is Benign according to our data. Variant chr6-1390041-CCCGCCGCCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 3041547.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 245 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2 link	c.115_123delGCCGCCGCC	p.Ala39_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENST00000645481.2	NP_001443.1	Q12947
FOXF2-DT	NR_189293.1 link	n.458+32_458+40delCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1 link	n.69-824_69-816delCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1 link	n.68+942_68+950delCGGCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 link	c.115_123delGCCGCCGCC	p.Ala39_Ala41del	conservative_inframe_deletion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1		Q12947

Frequencies

GnomAD3 genomes

AF:

0.00169

AC:

245

AN:

145194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00424

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00136

Gnomad ASJ

AF:

0.00206

Gnomad EAS

AF:

0.00103

Gnomad SAS

AF:

0.000213

Gnomad FIN

AF:

0.000468

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000502

Gnomad OTH

AF:

0.00249

GnomAD3 exomes

AF:

0.00167

AC:

AN:

34036

Hom.:

AF XY:

0.00147

AC XY:

AN XY:

19760

show subpopulations

Gnomad AFR exome

AF:

0.00962

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.00138

Gnomad EAS exome

AF:

0.00221

Gnomad SAS exome

AF:

0.00109

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00187

Gnomad OTH exome

AF:

0.00523

GnomAD4 exome

AF:

0.000686

AC:

830

AN:

1209318

Hom.:

AF XY:

0.000677

AC XY:

402

AN XY:

593744

show subpopulations

Gnomad4 AFR exome

AF:

0.00439

Gnomad4 AMR exome

AF:

0.00167

Gnomad4 ASJ exome

AF:

0.000778

Gnomad4 EAS exome

AF:

0.000347

Gnomad4 SAS exome

AF:

0.000798

Gnomad4 FIN exome

AF:

0.0000355

Gnomad4 NFE exome

AF:

0.000570

Gnomad4 OTH exome

AF:

0.000954

GnomAD4 genome

AF:

0.00169

AC:

245

AN:

145292

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

113

AN XY:

70768

show subpopulations

Gnomad4 AFR

AF:

0.00423

Gnomad4 AMR

AF:

0.00136

Gnomad4 ASJ

AF:

0.00206

Gnomad4 EAS

AF:

0.00103

Gnomad4 SAS

AF:

0.000213

Gnomad4 FIN

AF:

0.000468

Gnomad4 NFE

AF:

0.000502

Gnomad4 OTH

AF:

0.00247

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FOXF2-related disorder

Benign:1

Feb 09, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over