rs2241909

Variant names:

• chr17-8205021-G-A
• rs2241909
• NM_004217.4:c.885C>T
• AURKB p.Ser295Ser

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 35 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004217.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AURKB	NM_004217.4	MANE Select	c.885C>T	p.Ser295Ser	synonymous	Exon 9 of 9	NP_004208.2	Q96GD4-1
	AURKB	NM_001284526.2		c.888C>T	p.Ser296Ser	synonymous	Exon 9 of 9	NP_001271455.1	Q96GD4-5
	AURKB	NM_001313950.2		c.885C>T	p.Ser295Ser	synonymous	Exon 9 of 9	NP_001300879.1	Q96GD4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AURKB	ENST00000585124.6	TSL:1 MANE Select	c.885C>T	p.Ser295Ser	synonymous	Exon 9 of 9	ENSP00000463999.1	Q96GD4-1
	AURKB	ENST00000316199.10	TSL:1	c.888C>T	p.Ser296Ser	synonymous	Exon 9 of 9	ENSP00000313950.6	Q96GD4-5
	AURKB	ENST00000578549.5	TSL:1	c.789C>T	p.Ser263Ser	synonymous	Exon 8 of 8	ENSP00000462207.1	Q96GD4-2

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

GnomAD2 exomes AF: 0.657 AC: 151199 AN: 230290 AF XY: 0.659

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

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

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.7
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)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2241909;

hg19: chr17-8108339;

COSMIC: COSV60243958;

COSMIC: COSV60243958;