rs746176542
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr17-82519935-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG-C
- chr17-82519935-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG-CGGGCGGCGGGGCCGG
- chr17-82519935-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG
- chr17-82519935-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG-CGGGCGGCGGGGCCGGGGGCGGCGGGGCCGGGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM4BS2
The NM_004514.4(FOXK2):c.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG(p.Ala20_Gly29del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 982,646 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: 𝑓 0.000041 ( 0 hom., cov: 27)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
FOXK2
NM_004514.4 conservative_inframe_deletion
NM_004514.4 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.10
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_004514.4.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FOXK2 | NM_004514.4 | c.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG | p.Ala20_Gly29del | conservative_inframe_deletion | Exon 1 of 9 | ENST00000335255.10 | NP_004505.2 | |
| FOXK2 | XM_047435919.1 | c.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG | p.Ala20_Gly29del | conservative_inframe_deletion | Exon 1 of 9 | XP_047291875.1 | ||
| FOXK2 | XM_047435920.1 | c.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG | p.Ala20_Gly29del | conservative_inframe_deletion | Exon 1 of 5 | XP_047291876.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FOXK2 | ENST00000335255.10 | c.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG | p.Ala20_Gly29del | conservative_inframe_deletion | Exon 1 of 9 | 1 | NM_004514.4 | ENSP00000335677.5 | ||
| FOXK2 | ENST00000473637.6 | n.58_87delGCCGGGGGCGGCGGGGCCGGGGGCGGCGGG | non_coding_transcript_exon_variant | Exon 1 of 10 | 1 | ENSP00000436108.2 | ||||
| FOXK2 | ENST00000527313.6 | n.-41_-12delGGGCGGCGGGGCCGGGGGCGGCGGGGCCGG | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes 0.0000415 AC: 6AN: 144678Hom.: 0 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
144678
Hom.:
Cov.:
27
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: 0.0000119 AC: 10AN: 837968Hom.: 0 AF XY: 0.0000129 AC XY: 5AN XY: 387462 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
837968
Hom.:
AF XY:
AC XY:
5
AN XY:
387462
show subpopulations
African (AFR)
AF:
AC:
2
AN:
15876
American (AMR)
AF:
AC:
0
AN:
1202
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5258
East Asian (EAS)
AF:
AC:
0
AN:
3744
South Asian (SAS)
AF:
AC:
5
AN:
17136
European-Finnish (FIN)
AF:
AC:
0
AN:
614
Middle Eastern (MID)
AF:
AC:
0
AN:
1652
European-Non Finnish (NFE)
AF:
AC:
3
AN:
764884
Other (OTH)
AF:
AC:
0
AN:
27602
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000415 AC: 6AN: 144678Hom.: 0 Cov.: 27 AF XY: 0.0000142 AC XY: 1AN XY: 70312 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
144678
Hom.:
Cov.:
27
AF XY:
AC XY:
1
AN XY:
70312
show subpopulations
African (AFR)
AF:
AC:
3
AN:
40412
American (AMR)
AF:
AC:
0
AN:
14638
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3378
East Asian (EAS)
AF:
AC:
0
AN:
4960
South Asian (SAS)
AF:
AC:
2
AN:
4744
European-Finnish (FIN)
AF:
AC:
0
AN:
8124
Middle Eastern (MID)
AF:
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
AC:
1
AN:
65242
Other (OTH)
AF:
AC:
0
AN:
1986
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.583
Heterozygous variant carriers
0
1
1
2
2
3
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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