rs296565
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001252102.2(KIF21B):c.4615-16C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,610,992 control chromosomes in the GnomAD database, including 23,987 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1616 hom., cov: 33)
Exomes 𝑓: 0.17 ( 22371 hom. )
Consequence
KIF21B
NM_001252102.2 splice_polypyrimidine_tract, intron
NM_001252102.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.279
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 1-200974929-G-A is Benign according to our data. Variant chr1-200974929-G-A is described in ClinVar as [Benign]. Clinvar id is 1302458.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF21B | NM_001252102.2 | c.4615-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000461742.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF21B | ENST00000461742.7 | c.4615-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001252102.2 | P3 | |||
KIF21B | ENST00000332129.6 | c.4576-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
KIF21B | ENST00000360529.9 | c.4576-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
KIF21B | ENST00000422435.2 | c.4615-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.134 AC: 20341AN: 152094Hom.: 1615 Cov.: 33
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GnomAD3 exomes AF: 0.147 AC: 36576AN: 248338Hom.: 2979 AF XY: 0.152 AC XY: 20463AN XY: 134338
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GnomAD4 exome AF: 0.172 AC: 250415AN: 1458780Hom.: 22371 Cov.: 34 AF XY: 0.172 AC XY: 124889AN XY: 725720
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GnomAD4 genome ? AF: 0.134 AC: 20334AN: 152212Hom.: 1616 Cov.: 33 AF XY: 0.132 AC XY: 9822AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2021 | - - |
Computational scores
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Name
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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