rs17258783
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_194313.4(KIF24):c.*1281G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,536 control chromosomes in the GnomAD database, including 2,325 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2321 hom., cov: 32)
Exomes 𝑓: 0.16 ( 4 hom. )
Consequence
KIF24
NM_194313.4 3_prime_UTR
NM_194313.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.46
Genes affected
KIF24 (HGNC:19916): (kinesin family member 24) This gene encodes a member of the kinesin superfamily of microtubule-based motor proteins which are involved in the intracellular transport of membranous organelles, protein complexes, and mRNAs. They also play critical roles in mitosis, morphogenesis, and signal transduction. The encoded protein contains an N-terminal sterile alpha motif (SAM) domain and an ATP-binding kinesin motor domain. It binds centriolar coiled coil protein 110 and centrosomal protein 97 and localizes to the mother centriole to regulate ciliogenesis by controlling microtubule polymerization. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF24 | NM_194313.4 | c.*1281G>A | 3_prime_UTR_variant | 13/13 | ENST00000402558.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF24 | ENST00000402558.7 | c.*1281G>A | 3_prime_UTR_variant | 13/13 | 5 | NM_194313.4 | P1 | ||
KIF24 | ENST00000379174.7 | c.*1281G>A | 3_prime_UTR_variant | 9/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.158 AC: 24068AN: 152000Hom.: 2318 Cov.: 32
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GnomAD4 exome AF: 0.156 AC: 65AN: 418Hom.: 4 Cov.: 0 AF XY: 0.164 AC XY: 37AN XY: 226
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GnomAD4 genome ? AF: 0.158 AC: 24071AN: 152118Hom.: 2321 Cov.: 32 AF XY: 0.159 AC XY: 11813AN XY: 74322
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at