5-62348114-C-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001098511.3(KIF2A):c.226C>A(p.Pro76Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,613,658 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
Consequence
NM_001098511.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.226C>A | p.Pro76Thr | missense_variant | Exon 3 of 21 | ENST00000407818.8 | NP_001091981.1 | |
KIF2A | NM_004520.5 | c.226C>A | p.Pro76Thr | missense_variant | Exon 3 of 20 | NP_004511.2 | ||
KIF2A | NM_001243953.2 | c.226C>A | p.Pro76Thr | missense_variant | Exon 3 of 20 | NP_001230882.1 | ||
KIF2A | NM_001243952.2 | c.145C>A | p.Pro49Thr | missense_variant | Exon 4 of 21 | NP_001230881.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.226C>A | p.Pro76Thr | missense_variant | Exon 3 of 21 | 1 | NM_001098511.3 | ENSP00000385000.3 | ||
ENSG00000288643 | ENST00000509663.2 | n.64+41578C>A | intron_variant | Intron 1 of 5 | 3 | ENSP00000502199.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000315 AC: 79AN: 251128Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135708
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461550Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727060
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:1
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
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at