dbSNP rs6024840: AURKA:c.567-80T>C (chr20-56381651-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198437.3(AURKA):c.567-80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,564,156 control chromosomes in the GnomAD database, including 70,963 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 ( 10549 hom., cov: 32)

Exomes 𝑓: 0.28 ( 60414 hom. )

Consequence

AURKA
NM_198437.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

10 publications found

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]

AURKA Gene-Disease associations (from GenCC):

breast cancer
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
intellectual disability
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

AURKA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AURKA	NM_198437.3 link	c.567-80T>C		intron_variant	Intron 5 of 8	ENST00000395915.8	NP_940839.1	O14965

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AURKA	ENST00000395915.8 link	c.567-80T>C		intron_variant	Intron 5 of 8	1	NM_198437.3	ENSP00000379251.3		O14965

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53174

AN:

151944

Hom.:

10517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.688

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.335

GnomAD4 exome

AF:

0.278

AC:

392348

AN:

1412094

Hom.:

60414

AF XY:

0.279

AC XY:

196723

AN XY:

705078

show subpopulations

African (AFR)

AF:

0.506

AC:

16457

AN:

32506

American (AMR)

AF:

0.382

AC:

16922

AN:

44242

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

6705

AN:

25780

East Asian (EAS)

AF:

0.684

AC:

26727

AN:

39094

South Asian (SAS)

AF:

0.370

AC:

31246

AN:

84414

European-Finnish (FIN)

AF:

0.300

AC:

14017

AN:

46674

Middle Eastern (MID)

AF:

0.336

AC:

1626

AN:

4838

European-Non Finnish (NFE)

AF:

0.242

AC:

260775

AN:

1075886

Other (OTH)

AF:

0.305

AC:

17873

AN:

58660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13771

27542

41314

55085

68856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9084

18168

27252

36336

45420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.350

AC:

53258

AN:

152062

Hom.:

10549

Cov.:

AF XY:

0.354

AC XY:

26294

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.499

AC:

20673

AN:

41434

American (AMR)

AF:

0.327

AC:

4999

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

893

AN:

3468

East Asian (EAS)

AF:

0.688

AC:

3556

AN:

5170

South Asian (SAS)

AF:

0.383

AC:

1846

AN:

4824

European-Finnish (FIN)

AF:

0.312

AC:

3294

AN:

10570

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

16981

AN:

67996

Other (OTH)

AF:

0.333

AC:

701

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1671

3342

5014

6685

8356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.227

Hom.:

1066

Bravo

AF:

0.361

Asia WGS

AF:

0.524

AC:

1823

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.041

(source)

DANN

Benign

0.72

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over