Genetic Variant AURKB:c.48+309T>C (chr17-8209868-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_004217.4(AURKB):c.48+309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 464,038 control chromosomes in the GnomAD database, including 173,412 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 0.83 ( 52738 hom., cov: 29)

Exomes 𝑓: 0.88 ( 120674 hom. )

Consequence

AURKB
NM_004217.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298

Publications

8 publications found

Variant links:

Genes affected

AURKB (HGNC:11390): (aurora kinase B) This gene encodes a member of the aurora kinase subfamily of serine/threonine kinases. The genes encoding the other two members of this subfamily are located on chromosomes 19 and 20. These kinases participate in the regulation of alignment and segregation of chromosomes during mitosis and meiosis through association with microtubules. A pseudogene of this gene is located on chromosome 8. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]

AURKB links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AURKB	NM_004217.4 link	c.48+309T>C		intron_variant	Intron 2 of 8	ENST00000585124.6	NP_004208.2	Q96GD4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AURKB	ENST00000585124.6 link	c.48+309T>C		intron_variant	Intron 2 of 8	1	NM_004217.4	ENSP00000463999.1		Q96GD4-1

Frequencies

GnomAD3 genomes

AF:

0.829

AC:

125613

AN:

151460

Hom.:

52698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.706

Gnomad AMI

AF:

0.827

Gnomad AMR

AF:

0.830

Gnomad ASJ

AF:

0.729

Gnomad EAS

AF:

0.675

Gnomad SAS

AF:

0.868

Gnomad FIN

AF:

0.935

Gnomad MID

AF:

0.787

Gnomad NFE

AF:

0.902

Gnomad OTH

AF:

0.822

GnomAD4 exome

AF:

0.876

AC:

273731

AN:

312468

Hom.:

120674

AF XY:

0.876

AC XY:

142036

AN XY:

162068

show subpopulations

African (AFR)

AF:

0.705

AC:

5124

AN:

7264

American (AMR)

AF:

0.851

AC:

7680

AN:

9024

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

7778

AN:

10396

East Asian (EAS)

AF:

0.724

AC:

14748

AN:

20376

South Asian (SAS)

AF:

0.873

AC:

22546

AN:

25832

European-Finnish (FIN)

AF:

0.937

AC:

21779

AN:

23236

Middle Eastern (MID)

AF:

0.778

AC:

1179

AN:

1516

European-Non Finnish (NFE)

AF:

0.902

AC:

176468

AN:

195542

Other (OTH)

AF:

0.852

AC:

16429

AN:

19282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1490

2980

4471

5961

7451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.829

AC:

125699

AN:

151570

Hom.:

52738

Cov.:

AF XY:

0.831

AC XY:

61522

AN XY:

74038

show subpopulations

African (AFR)

AF:

0.706

AC:

29083

AN:

41188

American (AMR)

AF:

0.830

AC:

12664

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.729

AC:

2531

AN:

3470

East Asian (EAS)

AF:

0.675

AC:

3463

AN:

5128

South Asian (SAS)

AF:

0.869

AC:

4183

AN:

4816

European-Finnish (FIN)

AF:

0.935

AC:

9805

AN:

10492

Middle Eastern (MID)

AF:

0.788

AC:

230

AN:

292

European-Non Finnish (NFE)

AF:

0.902

AC:

61269

AN:

67922

Other (OTH)

AF:

0.819

AC:

1720

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1041

2082

3124

4165

5206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.876

Hom.:

85887

Bravo

AF:

0.816

Asia WGS

AF:

0.781

AC:

2711

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.5

(source)

DANN

Benign

0.81

PhyloP100

0.30

PromoterAI

0.017

Neutral

(source)

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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17-8209868-A-G

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