6-33402541-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002263.4(KIFC1):c.251-773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Consequence
KIFC1
NM_002263.4 intron
NM_002263.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.481
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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIFC1 | NM_002263.4 | c.251-773C>T | intron_variant | Intron 3 of 10 | ENST00000428849.7 | NP_002254.2 | ||
KIFC1 | XM_011514585.2 | c.251-773C>T | intron_variant | Intron 3 of 11 | XP_011512887.1 | |||
KIFC1 | XM_017010837.2 | c.128-773C>T | intron_variant | Intron 3 of 10 | XP_016866326.2 | |||
KIFC1 | XM_011514587.3 | c.251-773C>T | intron_variant | Intron 3 of 9 | XP_011512889.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIFC1 | ENST00000428849.7 | c.251-773C>T | intron_variant | Intron 3 of 10 | 1 | NM_002263.4 | ENSP00000393963.2 | |||
KIFC1 | ENST00000450504.1 | c.374-773C>T | intron_variant | Intron 4 of 6 | 3 | ENSP00000409539.1 | ||||
KIFC1 | ENST00000486695.1 | n.425-773C>T | intron_variant | Intron 1 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at