17-82520171-G-C
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_004514.4(FOXK2):c.283G>C(p.Ala95Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000676 in 1,478,356 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004514.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXK2 | NM_004514.4 | c.283G>C | p.Ala95Pro | missense_variant | Exon 1 of 9 | ENST00000335255.10 | NP_004505.2 | |
FOXK2 | XM_047435919.1 | c.283G>C | p.Ala95Pro | missense_variant | Exon 1 of 9 | XP_047291875.1 | ||
FOXK2 | XM_047435920.1 | c.283G>C | p.Ala95Pro | missense_variant | Exon 1 of 5 | XP_047291876.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXK2 | ENST00000335255.10 | c.283G>C | p.Ala95Pro | missense_variant | Exon 1 of 9 | 1 | NM_004514.4 | ENSP00000335677.5 | ||
FOXK2 | ENST00000473637.6 | n.283G>C | non_coding_transcript_exon_variant | Exon 1 of 10 | 1 | ENSP00000436108.2 | ||||
FOXK2 | ENST00000527313.6 | n.195G>C | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
FOXK2 | ENST00000570585.1 | n.-123G>C | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 150956Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00000796 AC: 1AN: 125600 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000678 AC: 9AN: 1327400Hom.: 0 Cov.: 33 AF XY: 0.00000912 AC XY: 6AN XY: 657980 show subpopulations
GnomAD4 genome AF: 0.00000662 AC: 1AN: 150956Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73650 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.283G>C (p.A95P) alteration is located in exon 1 (coding exon 1) of the FOXK2 gene. This alteration results from a G to C substitution at nucleotide position 283, causing the alanine (A) at amino acid position 95 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at