chr5-62348083-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001098511.3(KIF2A):c.195C>A(p.Asp65Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,613,756 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001098511.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.195C>A | p.Asp65Glu | missense_variant | 3/21 | ENST00000407818.8 | |
KIF2A | NM_004520.5 | c.195C>A | p.Asp65Glu | missense_variant | 3/20 | ||
KIF2A | NM_001243953.2 | c.195C>A | p.Asp65Glu | missense_variant | 3/20 | ||
KIF2A | NM_001243952.2 | c.114C>A | p.Asp38Glu | missense_variant | 4/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.195C>A | p.Asp65Glu | missense_variant | 3/21 | 1 | NM_001098511.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00627 AC: 954AN: 152158Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00158 AC: 397AN: 251154Hom.: 2 AF XY: 0.00119 AC XY: 161AN XY: 135728
GnomAD4 exome AF: 0.000629 AC: 919AN: 1461480Hom.: 9 Cov.: 30 AF XY: 0.000552 AC XY: 401AN XY: 727036
GnomAD4 genome ? AF: 0.00627 AC: 955AN: 152276Hom.: 8 Cov.: 32 AF XY: 0.00623 AC XY: 464AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 02, 2016 | 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. - |
KIF2A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 31, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at