rs2289883
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001098511.3(KIF2A):c.559-143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 512,836 control chromosomes in the GnomAD database, including 52,864 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.48 ( 18422 hom., cov: 32)
Exomes 𝑓: 0.43 ( 34442 hom. )
Consequence
KIF2A
NM_001098511.3 intron
NM_001098511.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.71
Genes affected
KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
DIMT1 (HGNC:30217): (DIM1 rRNA methyltransferase and ribosome maturation factor) The protein encoded by this gene is a methyltransferase that is responsible for dimethylation of adjacent adenosines near the 18S rRNA decoding site. The encoded protein is essential for ribosome biogenesis, although its catalytic activity is not involved in the process. The yeast ortholog of this protein functions in the cytoplasm while this protein functions in the nucleus. [provided by RefSeq, Jan 2017]
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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=-0.92).
BP6
?
Variant 5-62355016-G-A is Benign according to our data. Variant chr5-62355016-G-A is described in ClinVar as [Benign]. Clinvar id is 682867.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.559-143G>A | intron_variant | ENST00000407818.8 | |||
KIF2A | NM_001243952.2 | c.478-143G>A | intron_variant | ||||
KIF2A | NM_001243953.2 | c.502-143G>A | intron_variant | ||||
KIF2A | NM_004520.5 | c.559-143G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.559-143G>A | intron_variant | 1 | NM_001098511.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.481 AC: 73057AN: 151862Hom.: 18386 Cov.: 32
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GnomAD4 exome AF: 0.428 AC: 154491AN: 360856Hom.: 34442 AF XY: 0.423 AC XY: 80318AN XY: 189790
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GnomAD4 genome ? AF: 0.481 AC: 73147AN: 151980Hom.: 18422 Cov.: 32 AF XY: 0.481 AC XY: 35744AN XY: 74284
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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 | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational 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