rs3027260

Positions:

• chr17-8209868-A-G
• chr17-8209868-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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 -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/exons	MANE	UniProt
AURKB	NM_004217.4	c.48+309T>C		intron_variant		ENST00000585124.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AURKB	ENST00000585124.6	c.48+309T>C		intron_variant		1	NM_004217.4	P4

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125613 AN: 151460 Hom.: 52698 Cov.: 29

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

Gnomad4 AFR exome AF: 0.705

Gnomad4 AMR exome AF: 0.851

Gnomad4 ASJ exome AF: 0.748

Gnomad4 EAS exome AF: 0.724

Gnomad4 SAS exome AF: 0.873

Gnomad4 FIN exome AF: 0.937

Gnomad4 NFE exome AF: 0.902

Gnomad4 OTH exome AF: 0.852

GnomAD4 genome AF: 0.829 AC: 125699 AN: 151570 Hom.: 52738 Cov.: 29 AF XY: 0.831 AC XY: 61522 AN XY: 74038

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.819

Alfa AF: 0.882 Hom.: 66149

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
DANN	Benign	0.81

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: rs3027260; hg19: chr17-8113186;