1-26950708-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_152365.3(KDF1):c.1088G>A(p.Arg363Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000109 in 1,461,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152365.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDF1 | NM_152365.3 | c.1088G>A | p.Arg363Gln | missense_variant | Exon 3 of 4 | ENST00000320567.6 | NP_689578.2 | |
KDF1 | XM_005245735.3 | c.1088G>A | p.Arg363Gln | missense_variant | Exon 3 of 4 | XP_005245792.1 | ||
KDF1 | XM_011540622.3 | c.1088G>A | p.Arg363Gln | missense_variant | Exon 3 of 4 | XP_011538924.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251436Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135892
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461830Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1088G>A (p.R363Q) alteration is located in exon 3 (coding exon 2) of the KDF1 gene. This alteration results from a G to A substitution at nucleotide position 1088, causing the arginine (R) at amino acid position 363 to be replaced by a glutamine (Q). 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