9-114091992-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388308.1(KIF12):c.1825G>A(p.Gly609Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,611,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388308.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF12 | NM_001388308.1 | c.1825G>A | p.Gly609Arg | missense_variant | 19/19 | ENST00000640217.2 | NP_001375237.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF12 | ENST00000640217.2 | c.1825G>A | p.Gly609Arg | missense_variant | 19/19 | 5 | NM_001388308.1 | ENSP00000491702 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000489 AC: 12AN: 245424Hom.: 0 AF XY: 0.0000750 AC XY: 10AN XY: 133394
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1459138Hom.: 0 Cov.: 31 AF XY: 0.0000455 AC XY: 33AN XY: 725766
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74422
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 02, 2022 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 471 of the KIF12 protein (p.Gly471Arg). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with KIF12-related conditions. This variant is present in population databases (rs370618777, gnomAD 0.04%). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at