chr6-33398291-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002263.4(KIFC1):c.154C>T(p.Arg52Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,752 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
KIFC1
NM_002263.4 missense
NM_002263.4 missense
Scores
2
9
7
Clinical Significance
Conservation
PhyloP100: 2.57
Genes affected
KIFC1 (HGNC:6389): (kinesin family member C1) Predicted to enable microtubule binding activity and minus-end-directed microtubule motor activity. Involved in mitotic metaphase plate congression and mitotic spindle assembly. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIFC1 | NM_002263.4 | c.154C>T | p.Arg52Trp | missense_variant | 3/11 | ENST00000428849.7 | |
KIFC1 | XM_011514585.2 | c.154C>T | p.Arg52Trp | missense_variant | 3/12 | ||
KIFC1 | XM_017010837.2 | c.31C>T | p.Arg11Trp | missense_variant | 3/11 | ||
KIFC1 | XM_011514587.3 | c.154C>T | p.Arg52Trp | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFC1 | ENST00000428849.7 | c.154C>T | p.Arg52Trp | missense_variant | 3/11 | 1 | NM_002263.4 | P1 | |
KIFC1 | ENST00000450504.1 | c.154C>T | p.Arg52Trp | missense_variant | 3/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251492Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135920
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461814Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727216
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74184
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.154C>T (p.R52W) alteration is located in exon 3 (coding exon 3) of the KIFC1 gene. This alteration results from a C to T substitution at nucleotide position 154, causing the arginine (R) at amino acid position 52 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Benign
T;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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