6-1390041-CCCGCCGCCGCCGCCGCCGCCG-CCCG

Variant names:

• chr6-1390041-CCCGCCGCCGCCGCCGCCG-C
• rs747033801
• NM_001452.2:c.106_123delGCCGCCGCCGCCGCCGCC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001452.2(FOXF2):​c.106_123delGCCGCCGCCGCCGCCGCC​(p.Ala36_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 0.0000303 in 1,354,830 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000034 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000030 (0 hom.)
• Consequence: FOXF2 NM_001452.2 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31
• Publications: 0 publications found

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]

LINC01394 (HGNC:50670): (long intergenic non-protein coding RNA 1394)

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 5 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001452.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXF2	NM_001452.2	MANE Select	c.106_123delGCCGCCGCCGCCGCCGCC	p.Ala36_Ala41del	conservative_inframe_deletion	Exon 1 of 2	NP_001443.1	Q12947
	FOXF2-DT	NR_189293.1		n.458+23_458+40delCGGCGGCGGCGGCGGCGG		intron	N/A
	FOXF2-DT	NR_189294.1		n.69-833_69-816delCGGCGGCGGCGGCGGCGG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXF2	ENST00000645481.2	MANE Select	c.106_123delGCCGCCGCCGCCGCCGCC	p.Ala36_Ala41del	conservative_inframe_deletion	Exon 1 of 2	ENSP00000496415.1	Q12947
	LINC01394	ENST00000721686.1		n.89+933_89+950delCGGCGGCGGCGGCGGCGG		intron	N/A
	LINC01394	ENST00000721687.1		n.69-833_69-816delCGGCGGCGGCGGCGGCGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000344 AC: 5 AN: 145200 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000499

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000304

Gnomad OTH AF: 0.000498

GnomAD4 exome AF: 0.0000298 AC: 36 AN: 1209532 Hom.: 0 AF XY: 0.0000303 AC XY: 18 AN XY: 593884

African (AFR) AF: 0.000123 AC: 3 AN: 24358

American (AMR) AF: 0.00 AC: 0 AN: 21586

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19290

East Asian (EAS) AF: 0.00 AC: 0 AN: 23048

South Asian (SAS) AF: 0.00 AC: 0 AN: 58908

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3422

European-Non Finnish (NFE) AF: 0.0000254 AC: 25 AN: 982492

Other (OTH) AF: 0.000166 AC: 8 AN: 48250

GnomAD4 genome AF: 0.0000344 AC: 5 AN: 145298 Hom.: 0 Cov.: 31 AF XY: 0.0000283 AC XY: 2 AN XY: 70768

African (AFR) AF: 0.0000497 AC: 2 AN: 40206

American (AMR) AF: 0.00 AC: 0 AN: 14708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3392

East Asian (EAS) AF: 0.00 AC: 0 AN: 4832

South Asian (SAS) AF: 0.00 AC: 0 AN: 4692

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8546

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.0000304 AC: 2 AN: 65730

Other (OTH) AF: 0.000494 AC: 1 AN: 2026

Alfa AF: 0.00 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3
Mutation Taster		=164/36	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs747033801; hg19: chr6-1390276;