rs6099126

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000395915.8(AURKA):​c.-5-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 1,119,980 control chromosomes in the GnomAD database, including 7,166 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 0.32 ( 3405 hom., cov: 0)
Exomes 𝑓: 0.048 ( 3761 hom. )

Consequence

AURKA
ENST00000395915.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.188
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AURKANM_198437.3 linkuse as main transcriptc.-5-45G>A intron_variant ENST00000395915.8 NP_940839.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AURKAENST00000395915.8 linkuse as main transcriptc.-5-45G>A intron_variant 1 NM_198437.3 ENSP00000379251 P1

Frequencies

GnomAD3 genomes
AF:
0.316
AC:
20158
AN:
63820
Hom.:
3397
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.0913
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.268
Gnomad EAS
AF:
0.0864
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.0213
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.0845
Gnomad OTH
AF:
0.281
GnomAD3 exomes
AF:
0.0561
AC:
14067
AN:
250872
Hom.:
1568
AF XY:
0.0495
AC XY:
6716
AN XY:
135750
show subpopulations
Gnomad AFR exome
AF:
0.410
Gnomad AMR exome
AF:
0.0434
Gnomad ASJ exome
AF:
0.107
Gnomad EAS exome
AF:
0.0228
Gnomad SAS exome
AF:
0.0370
Gnomad FIN exome
AF:
0.00518
Gnomad NFE exome
AF:
0.0254
Gnomad OTH exome
AF:
0.0569
GnomAD4 exome
AF:
0.0481
AC:
50766
AN:
1056054
Hom.:
3761
Cov.:
25
AF XY:
0.0475
AC XY:
24616
AN XY:
518440
show subpopulations
Gnomad4 AFR exome
AF:
0.468
Gnomad4 AMR exome
AF:
0.0723
Gnomad4 ASJ exome
AF:
0.174
Gnomad4 EAS exome
AF:
0.0517
Gnomad4 SAS exome
AF:
0.0702
Gnomad4 FIN exome
AF:
0.00974
Gnomad4 NFE exome
AF:
0.0280
Gnomad4 OTH exome
AF:
0.0909
GnomAD4 genome
AF:
0.316
AC:
20200
AN:
63926
Hom.:
3405
Cov.:
0
AF XY:
0.304
AC XY:
9486
AN XY:
31214
show subpopulations
Gnomad4 AFR
AF:
0.529
Gnomad4 AMR
AF:
0.222
Gnomad4 ASJ
AF:
0.268
Gnomad4 EAS
AF:
0.0871
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.0213
Gnomad4 NFE
AF:
0.0845
Gnomad4 OTH
AF:
0.275
Alfa
AF:
0.0567
Hom.:
889
Bravo
AF:
0.149
Asia WGS
AF:
0.0570
AC:
201
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
11
DANN
Benign
0.85

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6099126; hg19: chr20-54963303; COSMIC: COSV53858766; COSMIC: COSV53858766; API