chr16-86510604-A-ACGGCGGCGGCGG
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000262426.6(FOXF1):c.48_59dupCGGCGGCGGCGG(p.Gly17_Gly20dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000725 in 1,379,010 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Consequence
FOXF1
ENST00000262426.6 disruptive_inframe_insertion
ENST00000262426.6 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.451
Genes affected
FOXF1 (HGNC:3809): (forkhead box F1) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in the regulation of pulmonary genes as well as embryonic development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FOXF1 | NM_001451.3 | c.48_59dupCGGCGGCGGCGG | p.Gly17_Gly20dup | disruptive_inframe_insertion | 1/2 | ENST00000262426.6 | NP_001442.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FOXF1 | ENST00000262426.6 | c.48_59dupCGGCGGCGGCGG | p.Gly17_Gly20dup | disruptive_inframe_insertion | 1/2 | 1 | NM_001451.3 | ENSP00000262426.4 |
Frequencies
GnomAD3 genomes 0.0000200 AC: 3AN: 150204Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000570 AC: 7AN: 1228806Hom.: 0 Cov.: 34 AF XY: 0.00000666 AC XY: 4AN XY: 600744
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GnomAD4 genome 0.0000200 AC: 3AN: 150204Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73314
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
FOXF1-related disorder Uncertain:1
| Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 30, 2024 | The FOXF1 c.48_59dup12 variant is predicted to result in an in-frame duplication (p.Gly20_Gly23dup). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at