5-62306499-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001098511.3(KIF2A):c.27C>A(p.Ile9=) 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 (★). Synonymous variant affecting the same amino acid position (i.e. I9I) has been classified as Likely benign.
Frequency
Consequence
NM_001098511.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.27C>A | p.Ile9= | synonymous_variant | 1/21 | ENST00000407818.8 | |
KIF2A | NM_004520.5 | c.27C>A | p.Ile9= | synonymous_variant | 1/20 | ||
KIF2A | NM_001243953.2 | c.27C>A | p.Ile9= | synonymous_variant | 1/20 | ||
KIF2A | NM_001243952.2 | c.-258C>A | 5_prime_UTR_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.27C>A | p.Ile9= | synonymous_variant | 1/21 | 1 | NM_001098511.3 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000574 AC: 8AN: 1392874Hom.: 0 Cov.: 32 AF XY: 0.0000102 AC XY: 7AN XY: 686944
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at