rs41274464
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000377093.9(KIF1B):c.*2353G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 1,041,774 control chromosomes in the GnomAD database, including 392 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 0.019 ( 42 hom., cov: 31)
Exomes 𝑓: 0.026 ( 350 hom. )
Consequence
KIF1B
ENST00000377093.9 3_prime_UTR
ENST00000377093.9 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.276
Genes affected
KIF1B (HGNC:16636): (kinesin family member 1B) Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in chemical synaptic transmission; dense core granule cytoskeletal transport; and vesicle-mediated transport. Predicted to act upstream of or within mitochondrion transport along microtubule. Predicted to be located in cytoplasmic vesicle membrane and neuron projection. Predicted to be part of kinesin complex. Predicted to be active in several cellular components, including axon; dendrite; and microtubule. Implicated in Charcot-Marie-Tooth disease type 2A1; carcinoma (multiple); multiple sclerosis; neuroblastoma; and pheochromocytoma. Biomarker of hepatocellular carcinoma. [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=-0.58).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0188 (2855/152178) while in subpopulation NFE AF= 0.0279 (1898/68006). AF 95% confidence interval is 0.0269. There are 42 homozygotes in gnomad4. There are 1426 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 2855 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1B | NM_001365951.3 | c.2115+9754G>A | intron_variant | ENST00000676179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1B | ENST00000676179.1 | c.2115+9754G>A | intron_variant | NM_001365951.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2855AN: 152060Hom.: 42 Cov.: 31
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GnomAD4 exome AF: 0.0259 AC: 23030AN: 889596Hom.: 350 Cov.: 32 AF XY: 0.0259 AC XY: 10635AN XY: 410880
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GnomAD4 genome ? AF: 0.0188 AC: 2855AN: 152178Hom.: 42 Cov.: 31 AF XY: 0.0192 AC XY: 1426AN XY: 74390
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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