NM_001451.3:c.979+302C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001451.3(FOXF1):c.979+302C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,096 control chromosomes in the GnomAD database, including 23,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.55 ( 23408 hom., cov: 34)
Consequence
FOXF1
NM_001451.3 intron
NM_001451.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.355
Publications
2 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 veinsInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 16-86511850-C-G is Benign according to our data. Variant chr16-86511850-C-G is described in ClinVar as Benign. ClinVar VariationId is 1273451.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.
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.
Frequencies
GnomAD3 genomes 0.547 AC: 83147AN: 151978Hom.: 23389 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
83147
AN:
151978
Hom.:
Cov.:
34
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.547 AC: 83187AN: 152096Hom.: 23408 Cov.: 34 AF XY: 0.545 AC XY: 40544AN XY: 74354 show subpopulations
GnomAD4 genome
AF:
AC:
83187
AN:
152096
Hom.:
Cov.:
34
AF XY:
AC XY:
40544
AN XY:
74354
show subpopulations
African (AFR)
AF:
AC:
17633
AN:
41498
American (AMR)
AF:
AC:
9886
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
2176
AN:
3470
East Asian (EAS)
AF:
AC:
3987
AN:
5148
South Asian (SAS)
AF:
AC:
2000
AN:
4824
European-Finnish (FIN)
AF:
AC:
5767
AN:
10582
Middle Eastern (MID)
AF:
AC:
124
AN:
294
European-Non Finnish (NFE)
AF:
AC:
39873
AN:
67958
Other (OTH)
AF:
AC:
1209
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1957
3914
5872
7829
9786
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
720
1440
2160
2880
3600
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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