rs41289846
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000375712.4(KIF3B):c.*3009G>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 0.0305 in 152,666 control chromosomes in the GnomAD database, including 115 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 0.030 ( 112 hom., cov: 32)
Exomes 𝑓: 0.076 ( 3 hom. )
Consequence
KIF3B
ENST00000375712.4 3_prime_UTR
ENST00000375712.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.39
Genes affected
KIF3B (HGNC:6320): (kinesin family member 3B) The protein encoded by this gene acts as a heterodimer with kinesin family member 3A to aid in chromosome movement during mitosis and meiosis. The encoded protein is a plus end-directed microtubule motor and can interact with the SMC3 subunit of the cohesin complex. In addition, the encoded protein may be involved in the intracellular movement of membranous organelles. This protein and kinesin family member 3A form the kinesin II subfamily of the kinesin superfamily. [provided by RefSeq, Jul 2008]
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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=-0.85).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0304 (4623/152150) while in subpopulation NFE AF= 0.045 (3063/68016). AF 95% confidence interval is 0.0437. There are 112 homozygotes in gnomad4. There are 2309 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 112 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF3B | NM_004798.4 | c.*3009G>A | 3_prime_UTR_variant | 9/9 | ENST00000375712.4 | NP_004789.1 | ||
KIF3B | XM_047440589.1 | c.*3009G>A | 3_prime_UTR_variant | 9/9 | XP_047296545.1 | |||
KIF3B | XM_047440590.1 | c.*3009G>A | 3_prime_UTR_variant | 9/9 | XP_047296546.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF3B | ENST00000375712.4 | c.*3009G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_004798.4 | ENSP00000364864 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0304 AC: 4627AN: 152032Hom.: 113 Cov.: 32
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GnomAD4 exome AF: 0.0756 AC: 39AN: 516Hom.: 3 Cov.: 0 AF XY: 0.0693 AC XY: 23AN XY: 332
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GnomAD4 genome AF: 0.0304 AC: 4623AN: 152150Hom.: 112 Cov.: 32 AF XY: 0.0310 AC XY: 2309AN XY: 74368
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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