NM_015656.2:c.25T>C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_015656.2(KIF26A):c.25T>C(p.Cys9Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,263,378 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C9G) has been classified as Uncertain significance.
Frequency
Consequence
NM_015656.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF26A | ENST00000423312.7 | c.25T>C | p.Cys9Arg | missense_variant | Exon 1 of 15 | 5 | NM_015656.2 | ENSP00000388241.2 | ||
KIF26A | ENST00000697132.1 | c.139-296T>C | intron_variant | Intron 1 of 14 | ENSP00000513129.1 |
Frequencies
GnomAD3 genomes AF: 0.000600 AC: 91AN: 151584Hom.: 1 Cov.: 33
GnomAD4 exome AF: 0.000131 AC: 146AN: 1111686Hom.: 1 Cov.: 31 AF XY: 0.000140 AC XY: 74AN XY: 530150
GnomAD4 genome AF: 0.000600 AC: 91AN: 151692Hom.: 1 Cov.: 33 AF XY: 0.000566 AC XY: 42AN XY: 74160
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.25T>C (p.C9R) alteration is located in exon 1 (coding exon 1) of the KIF26A gene. This alteration results from a T to C substitution at nucleotide position 25, causing the cysteine (C) at amino acid position 9 to be replaced by an arginine (R). 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