6-33402541-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.481
Variant links:
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
KIFC1NM_002263.4 linkc.251-773C>T intron_variant Intron 3 of 10 ENST00000428849.7 NP_002254.2 Q9BW19A0A024RCS7
KIFC1XM_011514585.2 linkc.251-773C>T intron_variant Intron 3 of 11 XP_011512887.1
KIFC1XM_017010837.2 linkc.128-773C>T intron_variant Intron 3 of 10 XP_016866326.2
KIFC1XM_011514587.3 linkc.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
KIFC1ENST00000428849.7 linkc.251-773C>T intron_variant Intron 3 of 10 1 NM_002263.4 ENSP00000393963.2 Q9BW19
KIFC1ENST00000450504.1 linkc.374-773C>T intron_variant Intron 4 of 6 3 ENSP00000409539.1 A2AB20
KIFC1ENST00000486695.1 linkn.425-773C>T intron_variant Intron 1 of 3 3

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.80
DANN
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs28787657; hg19: chr6-33370318; API