5-62306499-C-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001098511.3(KIF2A):c.27C>A(p.Ile9Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000574 in 1,392,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Consequence
KIF2A
NM_001098511.3 synonymous
NM_001098511.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.862
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 Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 5-62306499-C-A is Benign according to our data. Variant chr5-62306499-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1559088.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.862 with no splicing effect.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.27C>A | p.Ile9Ile | synonymous_variant | 1/21 | ENST00000407818.8 | NP_001091981.1 | |
KIF2A | NM_004520.5 | c.27C>A | p.Ile9Ile | synonymous_variant | 1/20 | NP_004511.2 | ||
KIF2A | NM_001243953.2 | c.27C>A | p.Ile9Ile | synonymous_variant | 1/20 | NP_001230882.1 | ||
KIF2A | NM_001243952.2 | c.-258C>A | 5_prime_UTR_variant | 1/21 | NP_001230881.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.27C>A | p.Ile9Ile | synonymous_variant | 1/21 | 1 | NM_001098511.3 | ENSP00000385000.3 | ||
ENSG00000288643 | ENST00000509663.2 | n.27C>A | non_coding_transcript_exon_variant | 1/6 | 3 | ENSP00000502199.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000574 AC: 8AN: 1392874Hom.: 0 Cov.: 32 AF XY: 0.0000102 AC XY: 7AN XY: 686944
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jul 19, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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