rs16979865

chr20-56391090-A-C

Variant summary

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

The NM_198437.3(AURKA):c.-6+1078T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 152,336 control chromosomes in the GnomAD database, including 502 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 0.076 (502 hom., cov: 33)
• Consequence: AURKA NM_198437.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AURKA	NM_198437.3	c.-6+1078T>G		intron_variant		ENST00000395915.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AURKA	ENST00000395915.8	c.-6+1078T>G		intron_variant		1	NM_198437.3	P1

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11537 AN: 152218 Hom.: 502 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0807

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0758 AC: 11552 AN: 152336 Hom.: 502 Cov.: 33 AF XY: 0.0735 AC XY: 5472 AN XY: 74498

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0945

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0480

Gnomad4 FIN AF: 0.0341

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0703 Hom.: 100

Bravo AF: 0.0820

Asia WGS AF: 0.0350 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	12
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs16979865; hg19: chr20-54966146;