6-1390068-G-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001452.2(FOXF2):c.121G>T(p.Ala41Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00308 in 1,382,210 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 9 hom. )
Consequence
FOXF2
NM_001452.2 missense
NM_001452.2 missense
Scores
1
1
17
Clinical Significance
Conservation
PhyloP100: 0.660
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.010308832).
BP6
Variant 6-1390068-G-T is Benign according to our data. Variant chr6-1390068-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3045896.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 288 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXF2 | NM_001452.2 | c.121G>T | p.Ala41Ser | missense_variant | 1/2 | ENST00000645481.2 | NP_001443.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXF2 | ENST00000645481.2 | c.121G>T | p.Ala41Ser | missense_variant | 1/2 | NM_001452.2 | ENSP00000496415 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00192 AC: 288AN: 149642Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00128 AC: 97AN: 75792Hom.: 0 AF XY: 0.00135 AC XY: 59AN XY: 43762
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GnomAD4 exome AF: 0.00322 AC: 3970AN: 1232462Hom.: 9 Cov.: 28 AF XY: 0.00308 AC XY: 1873AN XY: 607400
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GnomAD4 genome AF: 0.00192 AC: 288AN: 149748Hom.: 0 Cov.: 32 AF XY: 0.00178 AC XY: 130AN XY: 73076
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
FOXF2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N
PrimateAI
Pathogenic
D
PROVEAN
Benign
.;N
REVEL
Benign
Sift
Benign
.;T
Sift4G
Benign
.;T
Polyphen
B;B
Vest4
0.092
MVP
0.81
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at