5-62306552-AGCCCCGCTGGCCCGCTCG-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001098511.3(KIF2A):c.64+23_64+40del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,542,952 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
KIF2A
NM_001098511.3 intron
NM_001098511.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.29
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 5-62306552-AGCCCCGCTGGCCCGCTCG-A is Benign according to our data. Variant chr5-62306552-AGCCCCGCTGGCCCGCTCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 1649643.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.64+23_64+40del | intron_variant | ENST00000407818.8 | |||
KIF2A | NM_001243952.2 | c.-221+23_-221+40del | intron_variant | ||||
KIF2A | NM_001243953.2 | c.64+23_64+40del | intron_variant | ||||
KIF2A | NM_004520.5 | c.64+23_64+40del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.64+23_64+40del | intron_variant | 1 | NM_001098511.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390742Hom.: 0 AF XY: 0.00000146 AC XY: 1AN XY: 686106
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at