rs12089839
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001252102.2(KIF21B):c.2077+490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,218 control chromosomes in the GnomAD database, including 297 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 0.043 ( 297 hom., cov: 33)
Consequence
KIF21B
NM_001252102.2 intron
NM_001252102.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.166
Genes affected
KIF21B (HGNC:29442): (kinesin family member 21B) This gene encodes a member of the kinesin superfamily. Kinesins are ATP-dependent microtubule-based motor proteins that are involved in the intracellular transport of membranous organelles. Single nucleotide polymorphisms in this gene are associated with inflammatory bowel disease and multiple sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF21B | NM_001252102.2 | c.2077+490C>T | intron_variant | ENST00000461742.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF21B | ENST00000461742.7 | c.2077+490C>T | intron_variant | 1 | NM_001252102.2 | P3 | |||
KIF21B | ENST00000332129.6 | c.2077+490C>T | intron_variant | 1 | |||||
KIF21B | ENST00000360529.9 | c.2077+490C>T | intron_variant | 1 | A2 | ||||
KIF21B | ENST00000422435.2 | c.2077+490C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0431 AC: 6556AN: 152100Hom.: 294 Cov.: 33
GnomAD3 genomes
?
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0433 AC: 6587AN: 152218Hom.: 297 Cov.: 33 AF XY: 0.0460 AC XY: 3426AN XY: 74440
GnomAD4 genome
?
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6587
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152218
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33
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3426
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74440
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367
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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