rs2241909

Positions:

• chr17-8205021-G-A
• chr17-8205021-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_004217.4(AURKB):​c.885C>T​(p.Ser295=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AURKB	NM_004217.4	c.885C>T	p.Ser295=	synonymous_variant	9/9	ENST00000585124.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AURKB	ENST00000585124.6	c.885C>T	p.Ser295=	synonymous_variant	9/9	1	NM_004217.4	P4

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96325 AN: 151476 Hom.: 30939 Cov.: 29

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

GnomAD3 exomes AF: 0.657 AC: 151199 AN: 230290 Hom.: 50006 AF XY: 0.659 AC XY: 82837 AN XY: 125792

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 SAS exome AF: 0.714

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.: 59 AF XY: 0.659 AC XY: 471124 AN XY: 714382

Gnomad4 AFR exome AF: 0.565

Gnomad4 AMR exome AF: 0.693

Gnomad4 ASJ exome AF: 0.516

Gnomad4 EAS exome AF: 0.567

Gnomad4 SAS exome AF: 0.710

Gnomad4 FIN exome AF: 0.748

Gnomad4 NFE exome AF: 0.659

Gnomad4 OTH exome AF: 0.639

GnomAD4 genome AF: 0.636 AC: 96375 AN: 151594 Hom.: 30950 Cov.: 29 AF XY: 0.642 AC XY: 47582 AN XY: 74090

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.629

Alfa AF: 0.641 Hom.: 20431

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
DANN	Benign	0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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

Other links and lift over

dbSNP: rs2241909; hg19: chr17-8108339; COSMIC: COSV60243958; COSMIC: COSV60243958;