rs9471077
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145027.6(KIF6):c.2428+2743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,926 control chromosomes in the GnomAD database, including 21,684 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 0.50 ( 21684 hom., cov: 32)
Consequence
KIF6
NM_145027.6 intron
NM_145027.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.40
Genes affected
KIF6 (HGNC:21202): (kinesin family member 6) This gene encodes a member of a family of molecular motors which are involved in intracellular transport of protein complexes, membrane organelles, and messenger ribonucleic acid along microtubules. Kinesins function as homodimeric molecules with two N-terminal head domains that move along microtubules and two C-terminal tail domains that interact with the transported cargo, either directly or indirectly, through adapter molecules. This gene is ubiquitously expressed in coronary arteries and other vascular tissue. A naturally occurring mutation in this gene is associated with coronary heart disease. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF6 | NM_145027.6 | c.2428+2743T>C | intron_variant | ENST00000287152.12 | |||
LOC105375047 | XR_926774.3 | n.436-1673A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF6 | ENST00000287152.12 | c.2428+2743T>C | intron_variant | 2 | NM_145027.6 | P1 | |||
KIF6 | ENST00000229913.9 | c.781+2743T>C | intron_variant | 1 | |||||
KIF6 | ENST00000458470.5 | c.2052+2743T>C | intron_variant | 1 | |||||
KIF6 | ENST00000394362.5 | c.730+2743T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.504 AC: 76474AN: 151808Hom.: 21665 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.504 AC: 76544AN: 151926Hom.: 21684 Cov.: 32 AF XY: 0.499 AC XY: 37036AN XY: 74240
GnomAD4 genome
?
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32
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37036
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74240
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2027
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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