rs1047972

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_198437.3(AURKA):​c.169A>T​(p.Ile57Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I57V) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

AURKA
NM_198437.3 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07512).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AURKANM_198437.3 linkc.169A>T p.Ile57Phe missense_variant Exon 3 of 9 ENST00000395915.8 NP_940839.1 O14965

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AURKAENST00000395915.8 linkc.169A>T p.Ile57Phe missense_variant Exon 3 of 9 1 NM_198437.3 ENSP00000379251.3 O14965

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
6.84e-7
AC:
1
AN:
1461892
Hom.:
0
Cov.:
88
AF XY:
0.00000138
AC XY:
1
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
6.4
DANN
Benign
0.86
DEOGEN2
Benign
0.014
.;.;.;.;.;.;.;.;T;.;T;T;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.054
.;.;.;.;.;.;.;T;T;T;T;T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.075
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.69
T
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.94
N;N;N;N;N;N;N;N;N;N;N;D;D
REVEL
Benign
0.072
Sift
Uncertain
0.0040
D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Benign
0.064
T;T;T;T;T;T;T;D;.;.;.;.;.
Polyphen
0.33, 0.21, 0.057, 0.045, 0.0
.;.;.;.;.;.;.;B;B;B;B;B;.
Vest4
0.13
MutPred
0.13
Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);Loss of MoRF binding (P = 0.0873);
MVP
0.35
ClinPred
0.41
T
GERP RS
2.0
gMVP
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-54961463; API