rs9364385
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030615.4(KIF25):c.-162-3281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,052 control chromosomes in the GnomAD database, including 9,347 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 9347 hom., cov: 34)
Consequence
KIF25
NM_030615.4 intron
NM_030615.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.438
Genes affected
KIF25 (HGNC:6390): (kinesin family member 25) The protein encoded by this gene is a member of the kinesin-like protein family. Protein family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. However, the particular function of this gene product has not yet been determined. Two alternatively spliced transcript variants which encode products have been described. Other splice variants have been found that lack exon 2 and the initiation codon for translation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF25 | NM_030615.4 | c.-162-3281G>A | intron_variant | Intron 4 of 12 | ENST00000643607.3 | NP_085118.2 | ||
KIF25 | NM_005355.5 | c.-162-3281G>A | intron_variant | Intron 4 of 11 | NP_005346.3 | |||
KIF25 | XM_047418749.1 | c.-162-3281G>A | intron_variant | Intron 2 of 10 | XP_047274705.1 | |||
KIF25 | XM_011535803.4 | c.-162-3281G>A | intron_variant | Intron 2 of 9 | XP_011534105.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF25 | ENST00000643607.3 | c.-162-3281G>A | intron_variant | Intron 4 of 12 | NM_030615.4 | ENSP00000496229.1 | ||||
KIF25 | ENST00000443060.6 | c.-162-3281G>A | intron_variant | Intron 1 of 9 | 5 | ENSP00000388878.2 | ||||
KIF25 | ENST00000652547.1 | c.-162-3281G>A | intron_variant | Intron 1 of 5 | ENSP00000498669.1 | |||||
KIF25 | ENST00000515361.5 | n.415-3281G>A | intron_variant | Intron 4 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52673AN: 151934Hom.: 9324 Cov.: 34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.347 AC: 52742AN: 152052Hom.: 9347 Cov.: 34 AF XY: 0.354 AC XY: 26344AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at