6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCG

Variant names:

• chr6-1390041-CCCGCCGCCGCCGCCG-C
• rs747033801
• NM_001452.2:c.109_123delGCCGCCGCCGCCGCC

Variant summary

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

The NM_001452.2(FOXF2):​c.109_123delGCCGCCGCCGCCGCC​(p.Ala37_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 0.000311 in 1,354,798 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00048 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00029 (0 hom.)
• Consequence: FOXF2 NM_001452.2 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 70 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.109_123delGCCGCCGCCGCCGCC	p.Ala37_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENST00000645481.2	NP_001443.1
FOXF2-DT	NR_189293.1	n.458+26_458+40delCGGCGGCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1	n.69-830_69-816delCGGCGGCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1	n.68+936_68+950delCGGCGGCGGCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.109_123delGCCGCCGCCGCCGCC	p.Ala37_Ala41del	conservative_inframe_deletion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.000482 AC: 70 AN: 145200 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00177

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000206

Gnomad SAS AF: 0.000213

Gnomad FIN AF: 0.000234

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000289

Gnomad OTH AF: 0.000996

GnomAD3 exomes AF: 0.000441 AC: 15 AN: 34036 Hom.: 0 AF XY: 0.000658 AC XY: 13 AN XY: 19760

Gnomad AFR exome AF: 0.00240

Gnomad AMR exome AF: 0.00107

Gnomad ASJ exome AF: 0.000346

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000753

Gnomad NFE exome AF: 0.000163

Gnomad OTH exome AF: 0.00209

GnomAD4 exome AF: 0.000290 AC: 351 AN: 1209500 Hom.: 0 AF XY: 0.000286 AC XY: 170 AN XY: 593856

Gnomad4 AFR exome AF: 0.000411

Gnomad4 AMR exome AF: 0.000463

Gnomad4 ASJ exome AF: 0.0000519

Gnomad4 EAS exome AF: 0.000130

Gnomad4 SAS exome AF: 0.000204

Gnomad4 FIN exome AF: 0.000568

Gnomad4 NFE exome AF: 0.000273

Gnomad4 OTH exome AF: 0.000622

GnomAD4 genome AF: 0.000482 AC: 70 AN: 145298 Hom.: 0 Cov.: 31 AF XY: 0.000622 AC XY: 44 AN XY: 70768

Gnomad4 AFR AF: 0.000473

Gnomad4 AMR AF: 0.00177

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000207

Gnomad4 SAS AF: 0.000213

Gnomad4 FIN AF: 0.000234

Gnomad4 NFE AF: 0.000289

Gnomad4 OTH AF: 0.000987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747033801; hg19: chr6-1390276;