1-245367018-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_018012.4(KIF26B):c.650C>T(p.Ser217Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,611,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S217S) has been classified as Likely benign.
Frequency
Consequence
NM_018012.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26B | NM_018012.4 | c.650C>T | p.Ser217Leu | missense_variant | 3/15 | ENST00000407071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26B | ENST00000407071.7 | c.650C>T | p.Ser217Leu | missense_variant | 3/15 | 1 | NM_018012.4 | A2 | |
KIF26B | ENST00000479506.1 | n.424C>T | non_coding_transcript_exon_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241756Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131822
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459244Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 725772
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.650C>T (p.S217L) alteration is located in exon 3 (coding exon 3) of the KIF26B gene. This alteration results from a C to T substitution at nucleotide position 650, causing the serine (S) at amino acid position 217 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