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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001452.2(FOXF2):c.118_123dupGCCGCC(p.Ala40_Ala41dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000644 in 1,354,840 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00059 ( 1 hom. )

Consequence

FOXF2
NM_001452.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAd4 at 156 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2 link	c.118_123dupGCCGCC	p.Ala40_Ala41dup	conservative_inframe_insertion	Exon 1 of 2	ENST00000645481.2	NP_001443.1	Q12947
FOXF2-DT	NR_189293.1 link	n.458+35_458+40dupCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1 link	n.69-821_69-816dupCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1 link	n.68+945_68+950dupCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 link	c.118_123dupGCCGCC	p.Ala40_Ala41dup	conservative_inframe_insertion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1		Q12947

Frequencies

GnomAD3 genomes

AF:

0.00106

AC:

154

AN:

145198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000340

Gnomad ASJ

AF:

0.00147

Gnomad EAS

AF:

0.00124

Gnomad SAS

AF:

0.000639

Gnomad FIN

AF:

0.000117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00105

Gnomad OTH

AF:

0.00149

GnomAD4 exome

AF:

0.000593

AC:

717

AN:

1209544

Hom.:

Cov.:

AF XY:

0.000616

AC XY:

366

AN XY:

593884

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.000417

Gnomad4 ASJ exome

AF:

0.00161

Gnomad4 EAS exome

AF:

0.000824

Gnomad4 SAS exome

AF:

0.000221

Gnomad4 FIN exome

AF:

0.0000355

Gnomad4 NFE exome

AF:

0.000587

Gnomad4 OTH exome

AF:

0.000622

GnomAD4 genome

AF:

0.00107

AC:

156

AN:

145296

Hom.:

Cov.:

AF XY:

0.000933

AC XY:

AN XY:

70766

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.000272

Gnomad4 ASJ

AF:

0.00147

Gnomad4 EAS

AF:

0.00124

Gnomad4 SAS

AF:

0.000639

Gnomad4 FIN

AF:

0.000117

Gnomad4 NFE

AF:

0.00105

Gnomad4 OTH

AF:

0.00197

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over