chr6-1390850-GGGCGGC-G
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001452.2(FOXF2):c.914_919delGCGGCG(p.Gly305_Gly306del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000353 in 1,418,230 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 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000032 ( 0 hom. )
Consequence
FOXF2
NM_001452.2 disruptive_inframe_deletion
NM_001452.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.78
Publications
2 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)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FOXF2 | NM_001452.2 | c.914_919delGCGGCG | p.Gly305_Gly306del | disruptive_inframe_deletion | Exon 1 of 2 | ENST00000645481.2 | NP_001443.1 | |
| FOXF2-DT | NR_189294.1 | n.68+136_68+141delGCCGCC | intron_variant | Intron 1 of 2 | ||||
| FOXF2-DT | NR_189295.1 | n.68+136_68+141delGCCGCC | intron_variant | Intron 1 of 1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FOXF2 | ENST00000645481.2 | c.914_919delGCGGCG | p.Gly305_Gly306del | disruptive_inframe_deletion | Exon 1 of 2 | NM_001452.2 | ENSP00000496415.1 | |||
| LINC01394 | ENST00000721686.1 | n.89+136_89+141delGCCGCC | intron_variant | Intron 1 of 2 | ||||||
| LINC01394 | ENST00000721687.1 | n.68+136_68+141delGCCGCC | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes 0.00000661 AC: 1AN: 151336Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151336
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000316 AC: 4AN: 1266894Hom.: 0 AF XY: 0.00000323 AC XY: 2AN XY: 618672 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
4
AN:
1266894
Hom.:
AF XY:
AC XY:
2
AN XY:
618672
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
25056
American (AMR)
AF:
AC:
0
AN:
18662
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19176
East Asian (EAS)
AF:
AC:
0
AN:
29218
South Asian (SAS)
AF:
AC:
1
AN:
58360
European-Finnish (FIN)
AF:
AC:
0
AN:
31566
Middle Eastern (MID)
AF:
AC:
0
AN:
3832
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1028530
Other (OTH)
AF:
AC:
0
AN:
52494
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.009554), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.388
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000661 AC: 1AN: 151336Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 73922 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
151336
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
73922
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
41172
American (AMR)
AF:
AC:
0
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3460
East Asian (EAS)
AF:
AC:
0
AN:
5094
South Asian (SAS)
AF:
AC:
0
AN:
4814
European-Finnish (FIN)
AF:
AC:
0
AN:
10536
Middle Eastern (MID)
AF:
AC:
0
AN:
310
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67734
Other (OTH)
AF:
AC:
0
AN:
2086
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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