Variant 6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCG 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.112_123delGCCGCCGCCGCC(p.Ala38_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 0.000935 in 1,354,762 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00086 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00094 ( 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 6-1390041-CCCGCCGCCGCCG-C is Benign according to our data. Variant chr6-1390041-CCCGCCGCCGCCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 3047212.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 125 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2 link	c.112_123delGCCGCCGCCGCC	p.Ala38_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENST00000645481.2	NP_001443.1	Q12947
FOXF2-DT	NR_189293.1 link	n.458+29_458+40delCGGCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1 link	n.69-827_69-816delCGGCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1 link	n.68+939_68+950delCGGCGGCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 link	c.112_123delGCCGCCGCCGCC	p.Ala38_Ala41del	conservative_inframe_deletion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1		Q12947

Frequencies

GnomAD3 genomes

AF:

0.000861

AC:

125

AN:

145198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000324

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000681

Gnomad ASJ

AF:

0.000590

Gnomad EAS

AF:

0.00103

Gnomad SAS

AF:

0.000852

Gnomad FIN

AF:

0.000819

Gnomad MID

AF:

0.00338

Gnomad NFE

AF:

0.00140

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00209

AC:

AN:

34036

Hom.:

AF XY:

0.00152

AC XY:

AN XY:

19760

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000915

Gnomad ASJ exome

AF:

0.00381

Gnomad EAS exome

AF:

0.00221

Gnomad SAS exome

AF:

0.000136

Gnomad FIN exome

AF:

0.00301

Gnomad NFE exome

AF:

0.00342

Gnomad OTH exome

AF:

0.00105

GnomAD4 exome

AF:

0.000944

AC:

1142

AN:

1209466

Hom.:

AF XY:

0.000914

AC XY:

543

AN XY:

593834

show subpopulations

Gnomad4 AFR exome

AF:

0.000123

Gnomad4 AMR exome

AF:

0.000278

Gnomad4 ASJ exome

AF:

0.00197

Gnomad4 EAS exome

AF:

0.000347

Gnomad4 SAS exome

AF:

0.000374

Gnomad4 FIN exome

AF:

0.00110

Gnomad4 NFE exome

AF:

0.00102

Gnomad4 OTH exome

AF:

0.000663

GnomAD4 genome

AF:

0.000860

AC:

125

AN:

145296

Hom.:

Cov.:

AF XY:

0.000918

AC XY:

AN XY:

70768

show subpopulations

Gnomad4 AFR

AF:

0.000323

Gnomad4 AMR

AF:

0.0000680

Gnomad4 ASJ

AF:

0.000590

Gnomad4 EAS

AF:

0.00103

Gnomad4 SAS

AF:

0.000853

Gnomad4 FIN

AF:

0.000819

Gnomad4 NFE

AF:

0.00140

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FOXF2-related disorder

Benign:1

Sep 01, 2022

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