rs574179816

Variant names:

• chr16-86510604-ACGGCGGCGGCGGCGG-A
• rs574179816
• NM_001451.3:c.45_59delCGGCGGCGGCGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr16-86510604-ACGGCGGCGGCGGCGG-A
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGGCGG
• chr16-86510604-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGGCGGCGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001451.3(FOXF1):​c.45_59delCGGCGGCGGCGGCGG​(p.Gly16_Gly20del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000326 in 1,228,802 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: FOXF1 NM_001451.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 0 publications found

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]

FOXF1 Gene-Disease associations (from GenCC):

• alveolar capillary dysplasia with misalignment of pulmonary veins

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001451.3. 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
	FOXF1	NM_001451.3	MANE Select	c.45_59delCGGCGGCGGCGGCGG	p.Gly16_Gly20del	disruptive_inframe_deletion	Exon 1 of 2	NP_001442.2	Q12946

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXF1	ENST00000262426.6	TSL:1 MANE Select	c.45_59delCGGCGGCGGCGGCGG	p.Gly16_Gly20del	disruptive_inframe_deletion	Exon 1 of 2	ENSP00000262426.4	Q12946

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000326 AC: 4 AN: 1228802 Hom.: 0 AF XY: 0.00000333 AC XY: 2 AN XY: 600740

African (AFR) AF: 0.00 AC: 0 AN: 23790

American (AMR) AF: 0.00 AC: 0 AN: 11738

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17124

East Asian (EAS) AF: 0.00 AC: 0 AN: 28568

South Asian (SAS) AF: 0.00 AC: 0 AN: 49716

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36174

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3766

European-Non Finnish (NFE) AF: 0.00000397 AC: 4 AN: 1007830

Other (OTH) AF: 0.00 AC: 0 AN: 50096

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs574179816; hg19: chr16-86544210;