NM_004514.4:c.1382C>T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004514.4(FOXK2):c.1382C>T(p.Ser461Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000423 in 1,612,802 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152218Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000293 AC: 73AN: 249406 AF XY: 0.000340 show subpopulations
GnomAD4 exome AF: 0.000416 AC: 607AN: 1460466Hom.: 2 Cov.: 32 AF XY: 0.000423 AC XY: 307AN XY: 726516 show subpopulations
GnomAD4 genome AF: 0.000492 AC: 75AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000550 AC XY: 41AN XY: 74494 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1382C>T (p.S461L) alteration is located in exon 7 (coding exon 7) of the FOXK2 gene. This alteration results from a C to T substitution at nucleotide position 1382, causing the serine (S) at amino acid position 461 to be replaced by a leucine (L). 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