6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCGCCG

Variant names:

• chr6-1390041-CCCGCCG-C
• rs747033801
• NM_001452.2:c.118_123delGCCGCC

Variant summary

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

The NM_001452.2(FOXF2):​c.118_123delGCCGCC​(p.Ala40_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 0.00137 in 1,352,428 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0023 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0013 (2 hom.)
• Consequence: FOXF2 NM_001452.2 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

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 332 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.118_123delGCCGCC	p.Ala40_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENST00000645481.2	NP_001443.1
FOXF2-DT	NR_189293.1	n.458+35_458+40delCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1	n.69-821_69-816delCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1	n.68+945_68+950delCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.118_123delGCCGCC	p.Ala40_Ala41del	conservative_inframe_deletion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.00229 AC: 332 AN: 145192 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00551

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000204

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000825

Gnomad SAS AF: 0.00192

Gnomad FIN AF: 0.00140

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00120

Gnomad OTH AF: 0.00199

GnomAD3 exomes AF: 0.00194 AC: 66 AN: 34036 Hom.: 0 AF XY: 0.00218 AC XY: 43 AN XY: 19760

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000610

Gnomad ASJ exome AF: 0.000346

Gnomad EAS exome AF: 0.00221

Gnomad SAS exome AF: 0.00272

Gnomad FIN exome AF: 0.000753

Gnomad NFE exome AF: 0.00301

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00126 AC: 1515 AN: 1207138 Hom.: 2 AF XY: 0.00129 AC XY: 762 AN XY: 592582

Gnomad4 AFR exome AF: 0.00567

Gnomad4 AMR exome AF: 0.000652

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000695

Gnomad4 SAS exome AF: 0.00170

Gnomad4 FIN exome AF: 0.000748

Gnomad4 NFE exome AF: 0.00117

Gnomad4 OTH exome AF: 0.00154

GnomAD4 genome AF: 0.00229 AC: 332 AN: 145290 Hom.: 1 Cov.: 31 AF XY: 0.00215 AC XY: 152 AN XY: 70760

Gnomad4 AFR AF: 0.00552

Gnomad4 AMR AF: 0.000204

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000828

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.00140

Gnomad4 NFE AF: 0.00120

Gnomad4 OTH AF: 0.00197

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;