rs398686
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004521.3(KIF5B):c.1374+139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 674,742 control chromosomes in the GnomAD database, including 17,201 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 0.21 ( 3616 hom., cov: 32)
Exomes 𝑓: 0.22 ( 13585 hom. )
Consequence
KIF5B
NM_004521.3 intron
NM_004521.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.106
Genes affected
KIF5B (HGNC:6324): (kinesin family member 5B) Enables identical protein binding activity; microtubule binding activity; and microtubule motor activity. Involved in several processes, including lysosome localization; natural killer cell mediated cytotoxicity; and positive regulation of protein localization to plasma membrane. Located in centriolar satellite; cytosol; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF5B | NM_004521.3 | c.1374+139G>A | intron_variant | ENST00000302418.5 | NP_004512.1 | |||
KIF5B | XM_047425202.1 | c.1374+139G>A | intron_variant | XP_047281158.1 | ||||
KIF5B | XM_047425203.1 | c.1092+139G>A | intron_variant | XP_047281159.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF5B | ENST00000302418.5 | c.1374+139G>A | intron_variant | 1 | NM_004521.3 | ENSP00000307078 | P1 |
Frequencies
GnomAD3 genomes AF: 0.212 AC: 32230AN: 151966Hom.: 3607 Cov.: 32
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GnomAD4 exome AF: 0.216 AC: 113092AN: 522658Hom.: 13585 AF XY: 0.217 AC XY: 60792AN XY: 279910
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GnomAD4 genome AF: 0.212 AC: 32277AN: 152084Hom.: 3616 Cov.: 32 AF XY: 0.208 AC XY: 15439AN XY: 74330
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at