rs2296224
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001122819.3(KIF17):c.2020-39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00862 in 1,513,474 control chromosomes in the GnomAD database, including 83 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 0.0099 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 73 hom. )
Consequence
KIF17
NM_001122819.3 intron
NM_001122819.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.254
Genes affected
KIF17 (HGNC:19167): (kinesin family member 17) Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in anterograde dendritic transport of neurotransmitter receptor complex and cell projection organization. Predicted to act upstream of or within microtubule-based process; protein-containing complex localization; and vesicle-mediated transport. Predicted to be located in microtubule cytoskeleton. Predicted to be part of intraciliary transport particle B and kinesin complex. Predicted to be active in cilium; microtubule cytoskeleton; and neuron projection. [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=-0.82).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00988 (1505/152262) while in subpopulation EAS AF= 0.0283 (146/5160). AF 95% confidence interval is 0.0246. There are 10 homozygotes in gnomad4. There are 772 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF17 | NM_001122819.3 | c.2020-39G>A | intron_variant | ENST00000400463.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF17 | ENST00000400463.8 | c.2020-39G>A | intron_variant | 1 | NM_001122819.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00987 AC: 1502AN: 152144Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00950 AC: 1483AN: 156056Hom.: 13 AF XY: 0.00931 AC XY: 776AN XY: 83352
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GnomAD4 exome AF: 0.00848 AC: 11540AN: 1361212Hom.: 73 Cov.: 25 AF XY: 0.00854 AC XY: 5758AN XY: 674532
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GnomAD4 genome ? AF: 0.00988 AC: 1505AN: 152262Hom.: 10 Cov.: 32 AF XY: 0.0104 AC XY: 772AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
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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