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

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001452.2(FOXF2):c.121_123delGCC(p.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 0.0198 in 1,247,212 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 31)

Exomes 𝑓: 0.022 ( 1 hom. )

Consequence

FOXF2
NM_001452.2 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.89

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 Benign. Variant got -9 ACMG points.

BP6

Variant 6-1390041-CCCG-C is Benign according to our data. Variant chr6-1390041-CCCG-C is described in ClinVar as [Benign]. Clinvar id is 3055285.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2 link	c.121_123delGCC	p.Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENST00000645481.2	NP_001443.1	Q12947
FOXF2-DT	NR_189293.1 link	n.458+38_458+40delCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1 link	n.69-818_69-816delCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1 link	n.68+948_68+950delCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 link	c.121_123delGCC	p.Ala41del	conservative_inframe_deletion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1		Q12947

Frequencies

GnomAD3 genomes

AF:

0.00123

AC:

179

AN:

145168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00322

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00109

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000213

Gnomad FIN

AF:

0.00105

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000350

Gnomad OTH

AF:

0.000499

GnomAD3 exomes

AF:

0.0667

AC:

2269

AN:

34036

Hom.:

AF XY:

0.0660

AC XY:

1304

AN XY:

19760

show subpopulations

Gnomad AFR exome

AF:

0.0457

Gnomad AMR exome

AF:

0.0721

Gnomad ASJ exome

AF:

0.0713

Gnomad EAS exome

AF:

0.0940

Gnomad SAS exome

AF:

0.0683

Gnomad FIN exome

AF:

0.0520

Gnomad NFE exome

AF:

0.0637

Gnomad OTH exome

AF:

0.0649

GnomAD4 exome

AF:

0.0222

AC:

24507

AN:

1101948

Hom.:

AF XY:

0.0236

AC XY:

12580

AN XY:

533458

show subpopulations

Gnomad4 AFR exome

AF:

0.0239

Gnomad4 AMR exome

AF:

0.0486

Gnomad4 ASJ exome

AF:

0.0327

Gnomad4 EAS exome

AF:

0.0197

Gnomad4 SAS exome

AF:

0.0582

Gnomad4 FIN exome

AF:

0.0383

Gnomad4 NFE exome

AF:

0.0192

Gnomad4 OTH exome

AF:

0.0251

GnomAD4 genome

AF:

0.00127

AC:

184

AN:

145264

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

AN XY:

70750

show subpopulations

Gnomad4 AFR

AF:

0.00333

Gnomad4 AMR

AF:

0.00109

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000213

Gnomad4 FIN

AF:

0.00105

Gnomad4 NFE

AF:

0.000350

Gnomad4 OTH

AF:

0.000494

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FOXF2-related disorder

Benign:1

Aug 01, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as 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

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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