dbSNP rs2241909: AURKB:p.Ser295Ser (chr17-8205021-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004217.4(AURKB):c.885C>T(p.Ser295Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 1,588,274 control chromosomes in the GnomAD database, including 343,908 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 0.64 ( 30950 hom., cov: 29)

Exomes 𝑓: 0.66 ( 312958 hom. )

Consequence

AURKB
NM_004217.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.761

Publications

35 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-0.761 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AURKB	NM_004217.4 link	c.885C>T	p.Ser295Ser	synonymous_variant	Exon 9 of 9	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.885C>T	p.Ser295Ser	synonymous_variant	Exon 9 of 9	1	NM_004217.4	ENSP00000463999.1		Q96GD4-1

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

96325

AN:

151476

Hom.:

30939

Cov.:

show subpopulations

Gnomad AFR

AF:

0.570

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.754

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.663

Gnomad OTH

AF:

0.630

GnomAD2 exomes

AF:

0.657

AC:

151199

AN:

230290

AF XY:

0.659

show subpopulations

Gnomad AFR exome

AF:

0.562

Gnomad AMR exome

AF:

0.696

Gnomad ASJ exome

AF:

0.523

Gnomad EAS exome

AF:

0.507

Gnomad FIN exome

AF:

0.745

Gnomad NFE exome

AF:

0.662

Gnomad OTH exome

AF:

0.649

GnomAD4 exome

AF:

0.658

AC:

945839

AN:

1436680

Hom.:

312958

Cov.:

AF XY:

0.659

AC XY:

471124

AN XY:

714382

show subpopulations

African (AFR)

AF:

0.565

AC:

17851

AN:

31578

American (AMR)

AF:

0.693

AC:

25093

AN:

36212

Ashkenazi Jewish (ASJ)

AF:

0.516

AC:

12756

AN:

24720

East Asian (EAS)

AF:

0.567

AC:

22400

AN:

39512

South Asian (SAS)

AF:

0.710

AC:

60219

AN:

84786

European-Finnish (FIN)

AF:

0.748

AC:

39732

AN:

53134

Middle Eastern (MID)

AF:

0.586

AC:

3302

AN:

5632

European-Non Finnish (NFE)

AF:

0.659

AC:

726707

AN:

1101938

Other (OTH)

AF:

0.639

AC:

37779

AN:

59168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

17064

34127

51191

68254

85318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19000

38000

57000

76000

95000

<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:

0.636

AC:

96375

AN:

151594

Hom.:

30950

Cov.:

AF XY:

0.642

AC XY:

47582

AN XY:

74090

show subpopulations

African (AFR)

AF:

0.570

AC:

23512

AN:

41264

American (AMR)

AF:

0.657

AC:

10010

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.490

AC:

1699

AN:

3464

East Asian (EAS)

AF:

0.524

AC:

2673

AN:

5102

South Asian (SAS)

AF:

0.722

AC:

3472

AN:

4808

European-Finnish (FIN)

AF:

0.754

AC:

7965

AN:

10558

Middle Eastern (MID)

AF:

0.610

AC:

178

AN:

292

European-Non Finnish (NFE)

AF:

0.663

AC:

44989

AN:

67870

Other (OTH)

AF:

0.629

AC:

1320

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1773

3546

5318

7091

8864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.640

Hom.:

21416

Bravo

AF:

0.624

Asia WGS

AF:

0.635

AC:

2210

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.7

(source)

DANN

Benign

0.41

PhyloP100

-0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=99/1

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