rs6099119
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_198437.3(AURKA):c.*254T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00429 in 571,954 control chromosomes in the GnomAD database, including 39 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 0.012 ( 27 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 12 hom. )
Consequence
AURKA
NM_198437.3 3_prime_UTR
NM_198437.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.169
Genes affected
AURKA (HGNC:11393): (aurora kinase A) The protein encoded by this gene is a cell cycle-regulated kinase that appears to be involved in microtubule formation and/or stabilization at the spindle pole during chromosome segregation. The encoded protein is found at the centrosome in interphase cells and at the spindle poles in mitosis. This gene may play a role in tumor development and progression. A processed pseudogene of this gene has been found on chromosome 1, and an unprocessed pseudogene has been found on chromosome 10. Multiple transcript variants encoding the same protein have been found for this gene. [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=-0.81).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0116 (1768/152326) while in subpopulation AFR AF= 0.04 (1665/41574). AF 95% confidence interval is 0.0384. There are 27 homozygotes in gnomad4. There are 823 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1768 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AURKA | NM_198437.3 | c.*254T>C | 3_prime_UTR_variant | 9/9 | ENST00000395915.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AURKA | ENST00000395915.8 | c.*254T>C | 3_prime_UTR_variant | 9/9 | 1 | NM_198437.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0115 AC: 1754AN: 152208Hom.: 26 Cov.: 33
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GnomAD4 exome AF: 0.00163 AC: 685AN: 419628Hom.: 12 Cov.: 4 AF XY: 0.00140 AC XY: 311AN XY: 222638
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GnomAD4 genome ? AF: 0.0116 AC: 1768AN: 152326Hom.: 27 Cov.: 33 AF XY: 0.0110 AC XY: 823AN XY: 74490
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at