6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG

Variant names:

• chr6-1390041-C-CCCGCCGCCG
• rs747033801
• NM_001452.2:c.115_123dupGCCGCCGCC

Variant summary

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

The NM_001452.2(FOXF2):​c.115_123dupGCCGCCGCC​(p.Ala39_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 0.000137 in 1,354,886 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 0.00014 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00014 (0 hom.)
• Consequence: FOXF2 NM_001452.2 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

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 21 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.115_123dupGCCGCCGCC	p.Ala39_Ala41dup	conservative_inframe_insertion	Exon 1 of 2	ENST00000645481.2	NP_001443.1
FOXF2-DT	NR_189293.1	n.458+32_458+40dupCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189294.1	n.69-824_69-816dupCGGCGGCGG		intron_variant	Intron 1 of 2
FOXF2-DT	NR_189295.1	n.68+942_68+950dupCGGCGGCGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.115_123dupGCCGCCGCC	p.Ala39_Ala41dup	conservative_inframe_insertion	Exon 1 of 2		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.000145 AC: 21 AN: 145202 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000349

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000295

Gnomad EAS AF: 0.000206

Gnomad SAS AF: 0.000213

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000608

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000136 AC: 165 AN: 1209586 Hom.: 0 Cov.: 28 AF XY: 0.000108 AC XY: 64 AN XY: 593908

Gnomad4 AFR exome AF: 0.000328

Gnomad4 AMR exome AF: 0.0000463

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000868

Gnomad4 SAS exome AF: 0.000153

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000146

Gnomad4 OTH exome AF: 0.0000414

GnomAD4 genome AF: 0.000145 AC: 21 AN: 145300 Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 9 AN XY: 70770

Gnomad4 AFR AF: 0.000348

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000295

Gnomad4 EAS AF: 0.000207

Gnomad4 SAS AF: 0.000213

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000609

Gnomad4 OTH AF: 0.00

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;