chr9-34255825-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_194313.4(KIF24):c.3782G>C(p.Arg1261Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00527 in 1,613,914 control chromosomes in the GnomAD database, including 318 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 Benign (★).
Frequency
Genomes: 𝑓 0.026 ( 167 hom., cov: 32)
Exomes 𝑓: 0.0031 ( 151 hom. )
Consequence
KIF24
NM_194313.4 missense
NM_194313.4 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 1.94
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0020516813).
BP6
?
Variant 9-34255825-C-G is Benign according to our data. Variant chr9-34255825-C-G is described in ClinVar as [Benign]. Clinvar id is 774429.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF24 | NM_194313.4 | c.3782G>C | p.Arg1261Thr | missense_variant | 11/13 | ENST00000402558.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF24 | ENST00000402558.7 | c.3782G>C | p.Arg1261Thr | missense_variant | 11/13 | 5 | NM_194313.4 | P1 | |
KIF24 | ENST00000379174.7 | c.3380G>C | p.Arg1127Thr | missense_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0262 AC: 3992AN: 152126Hom.: 167 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00736 AC: 1848AN: 250992Hom.: 60 AF XY: 0.00537 AC XY: 729AN XY: 135656
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GnomAD4 exome AF: 0.00309 AC: 4511AN: 1461670Hom.: 151 Cov.: 32 AF XY: 0.00269 AC XY: 1954AN XY: 727118
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GnomAD4 genome ? AF: 0.0262 AC: 3990AN: 152244Hom.: 167 Cov.: 32 AF XY: 0.0258 AC XY: 1918AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
T;D
Polyphen
P;.
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
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