chr20-56386485-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_198437.3(AURKA):c.91T>A(p.Phe31Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,613,914 control chromosomes in the GnomAD database, including 50,544 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.22 ( 4562 hom., cov: 33)
Exomes 𝑓: 0.24 ( 45982 hom. )
Consequence
AURKA
NM_198437.3 missense
NM_198437.3 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -0.555
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=3.5131277E-6).
BP6
?
Variant 20-56386485-A-T is Benign according to our data. Variant chr20-56386485-A-T is described in ClinVar as [Benign]. Clinvar id is 6642.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AURKA | NM_198437.3 | c.91T>A | p.Phe31Ile | missense_variant | 3/9 | ENST00000395915.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AURKA | ENST00000395915.8 | c.91T>A | p.Phe31Ile | missense_variant | 3/9 | 1 | NM_198437.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.223 AC: 33952AN: 152018Hom.: 4556 Cov.: 33
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GnomAD3 exomes AF: 0.278 AC: 69789AN: 251444Hom.: 11713 AF XY: 0.274 AC XY: 37297AN XY: 135904
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GnomAD4 exome AF: 0.236 AC: 345594AN: 1461776Hom.: 45982 Cov.: 41 AF XY: 0.238 AC XY: 172899AN XY: 727194
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GnomAD4 genome ? AF: 0.223 AC: 33974AN: 152138Hom.: 4562 Cov.: 33 AF XY: 0.230 AC XY: 17118AN XY: 74378
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841
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848
ESP6500AA
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33184
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ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
AURKA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2020 | This variant is associated with the following publications: (PMID: 23803310, 21412660, 22213102, 15867347, 15271856, 21198377, 20002563, 17219423, 17898866, 24349361, 15087379, 28903390, 25697104) - |
Colon cancer, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Aug 01, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N;N;D;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T;.;.;.;.;.
Polyphen
0.0
.;.;.;.;.;.;.;B;B;B;B;B;.
Vest4
ClinPred
T
GERP RS
gMVP
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