rs2298016

Positions:

• chr20-56384240-G-C
• chr20-56384240-G-T

Variant summary

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

The ENST00000395915.8(AURKA):​c.374+30C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,555,324 control chromosomes in the GnomAD database, including 52,681 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 0.25 (5492 hom., cov: 32)
  • Exomes 𝑓: 0.24 (47189 hom.)
• Consequence: AURKA ENST00000395915.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

AURKA (HGNC:11393): (aurora kinase A) The protein encoded by this gene is a cell cycle-regulated kinase that appears to be involved in microtubule formation and/or stabilization at the spindle pole during chromosome segregation. The encoded protein is found at the centrosome in interphase cells and at the spindle poles in mitosis. This gene may play a role in tumor development and progression. A processed pseudogene of this gene has been found on chromosome 1, and an unprocessed pseudogene has been found on chromosome 10. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AURKA	NM_198437.3	c.374+30C>G		intron_variant		ENST00000395915.8	NP_940839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AURKA	ENST00000395915.8	c.374+30C>G		intron_variant		1	NM_198437.3	ENSP00000379251	P1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38500 AN: 151848 Hom.: 5477 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.253

GnomAD3 exomes AF: 0.292 AC: 72409 AN: 247606 Hom.: 12349 AF XY: 0.289 AC XY: 38704 AN XY: 134154

Gnomad AFR exome AF: 0.217

Gnomad AMR exome AF: 0.352

Gnomad ASJ exome AF: 0.164

Gnomad EAS exome AF: 0.672

Gnomad SAS exome AF: 0.331

Gnomad FIN exome AF: 0.293

Gnomad NFE exome AF: 0.226

Gnomad OTH exome AF: 0.260

GnomAD4 exome AF: 0.245 AC: 343407 AN: 1403358 Hom.: 47189 Cov.: 26 AF XY: 0.247 AC XY: 172971 AN XY: 701538

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.344

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.663

Gnomad4 SAS exome AF: 0.330

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.218

Gnomad4 OTH exome AF: 0.253

GnomAD4 genome AF: 0.254 AC: 38550 AN: 151966 Hom.: 5492 Cov.: 32 AF XY: 0.262 AC XY: 19430 AN XY: 74268

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.252

Alfa AF: 0.160 Hom.: 465

Bravo AF: 0.253

Asia WGS AF: 0.471 AC: 1630 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2298016; hg19: chr20-54959296; COSMIC: COSV57167229; COSMIC: COSV57167229;