rs2297909
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001252102.2(KIF21B):c.2455-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,581,260 control chromosomes in the GnomAD database, including 69,180 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 0.27 ( 5740 hom., cov: 33)
Exomes 𝑓: 0.30 ( 63440 hom. )
Consequence
KIF21B
NM_001252102.2 intron
NM_001252102.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.00
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF21B | NM_001252102.2 | c.2455-30C>T | intron_variant | ENST00000461742.7 | NP_001239031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF21B | ENST00000461742.7 | c.2455-30C>T | intron_variant | 1 | NM_001252102.2 | ENSP00000433808 | P3 | |||
KIF21B | ENST00000332129.6 | c.2455-30C>T | intron_variant | 1 | ENSP00000328494 | |||||
KIF21B | ENST00000360529.9 | c.2455-30C>T | intron_variant | 1 | ENSP00000353724 | A2 | ||||
KIF21B | ENST00000422435.2 | c.2455-30C>T | intron_variant | 1 | ENSP00000411831 |
Frequencies
GnomAD3 genomes AF: 0.270 AC: 41021AN: 151980Hom.: 5725 Cov.: 33
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GnomAD3 exomes AF: 0.265 AC: 58105AN: 219152Hom.: 7694 AF XY: 0.266 AC XY: 32098AN XY: 120712
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GnomAD4 exome AF: 0.295 AC: 421662AN: 1429162Hom.: 63440 Cov.: 27 AF XY: 0.292 AC XY: 207821AN XY: 710998
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GnomAD4 genome AF: 0.270 AC: 41061AN: 152098Hom.: 5740 Cov.: 33 AF XY: 0.266 AC XY: 19782AN XY: 74366
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at