rs2291395
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004514.4(FOXK2):c.762+62A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,583,410 control chromosomes in the GnomAD database, including 163,993 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 15310 hom., cov: 33)
Exomes 𝑓: 0.45 ( 148683 hom. )
Consequence
FOXK2
NM_004514.4 intron
NM_004514.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
Genes affected
FOXK2 (HGNC:6036): (forkhead box K2) The protein encoded by this gene contains a fork head DNA binding domain. This protein can bind to the purine-rich motifs of the HIV long terminal repeat (LTR), and to the similar purine-rich motif in the interleukin 2 (IL2) promoter. It may be involved in the regulation of viral and cellular promoter elements. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXK2 | NM_004514.4 | c.762+62A>G | intron_variant | ENST00000335255.10 | |||
FOXK2 | XM_047435919.1 | c.762+62A>G | intron_variant | ||||
FOXK2 | XM_047435920.1 | c.762+62A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXK2 | ENST00000335255.10 | c.762+62A>G | intron_variant | 1 | NM_004514.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.446 AC: 67797AN: 151890Hom.: 15292 Cov.: 33
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GnomAD4 exome AF: 0.455 AC: 651276AN: 1431400Hom.: 148683 AF XY: 0.459 AC XY: 326878AN XY: 712758
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GnomAD4 genome ? AF: 0.446 AC: 67856AN: 152010Hom.: 15310 Cov.: 33 AF XY: 0.449 AC XY: 33335AN XY: 74324
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at