chrX-70330186-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BP6BS2
The NM_012310.5(KIF4A):c.925A>T(p.Met309Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000332 in 1,206,092 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012310.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF4A | NM_012310.5 | c.925A>T | p.Met309Leu | missense_variant | 9/31 | ENST00000374403.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF4A | ENST00000374403.4 | c.925A>T | p.Met309Leu | missense_variant | 9/31 | 1 | NM_012310.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 3AN: 111604Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33794
GnomAD3 exomes AF: 0.000195 AC: 35AN: 179099Hom.: 0 AF XY: 0.000141 AC XY: 9AN XY: 63921
GnomAD4 exome AF: 0.0000338 AC: 37AN: 1094488Hom.: 0 Cov.: 28 AF XY: 0.0000278 AC XY: 10AN XY: 360248
GnomAD4 genome ? AF: 0.0000269 AC: 3AN: 111604Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33794
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.925A>T (p.M309L) alteration is located in exon 9 (coding exon 8) of the KIF4A gene. This alteration results from a A to T substitution at nucleotide position 925, causing the methionine (M) at amino acid position 309 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
KIF4A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2022 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at