rs536166099
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144508.5(KNL1):c.6796C>A(p.Pro2266Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2266A) has been classified as Uncertain significance.
Frequency
Consequence
NM_144508.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KNL1 | NM_144508.5 | c.6796C>A | p.Pro2266Thr | missense_variant | 25/26 | ENST00000399668.7 | |
KNL1 | NM_170589.5 | c.6874C>A | p.Pro2292Thr | missense_variant | 26/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNL1 | ENST00000399668.7 | c.6796C>A | p.Pro2266Thr | missense_variant | 25/26 | 1 | NM_144508.5 | A2 | |
KNL1 | ENST00000346991.9 | c.6874C>A | p.Pro2292Thr | missense_variant | 26/27 | 1 | P4 | ||
KNL1 | ENST00000526913.5 | c.3931C>A | p.Pro1311Thr | missense_variant, NMD_transcript_variant | 16/18 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249556Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135392
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461522Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727094
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152302Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74466
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at