9-34256489-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_194313.4(KIF24):c.3118A>T(p.Thr1040Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194313.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF24 | NM_194313.4 | c.3118A>T | p.Thr1040Ser | missense_variant | 11/13 | ENST00000402558.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF24 | ENST00000402558.7 | c.3118A>T | p.Thr1040Ser | missense_variant | 11/13 | 5 | NM_194313.4 | P1 | |
KIF24 | ENST00000379174.7 | c.2716A>T | p.Thr906Ser | missense_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250926Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135592
GnomAD4 exome AF: 0.000104 AC: 152AN: 1461574Hom.: 0 Cov.: 36 AF XY: 0.0000935 AC XY: 68AN XY: 727070
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.3118A>T (p.T1040S) alteration is located in exon 11 (coding exon 10) of the KIF24 gene. This alteration results from a A to T substitution at nucleotide position 3118, causing the threonine (T) at amino acid position 1040 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at