Variant chr19-57231699-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000302804.12(AURKC):c.59-43C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,609,416 control chromosomes in the GnomAD database, including 85,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8213 hom., cov: 28)

Exomes 𝑓: 0.32 ( 77038 hom. )

Consequence

AURKC
ENST00000302804.12 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.326

Variant links:

Genes affected

AURKC (HGNC:11391): (aurora kinase C) This gene encodes a member of the Aurora subfamily of serine/threonine protein kinases. The encoded protein is a chromosomal passenger protein that forms complexes with Aurora-B and inner centromere proteins and may play a role in organizing microtubules in relation to centrosome/spindle function during mitosis. This gene is overexpressed in several cancer cell lines, suggesting an involvement in oncogenic signal transduction. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

AURKC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 19-57231699-C-G is Benign according to our data. Variant chr19-57231699-C-G is described in ClinVar as [Benign]. Clinvar id is 1262537.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
AURKC	NM_001015878.2 linkuse as main transcript	c.59-43C>G	intron_variant	ENST00000302804.12	NP_001015878.1
AURKC	NM_001015879.2 linkuse as main transcript	c.2-43C>G	intron_variant		NP_001015879.1
AURKC	NM_003160.3 linkuse as main transcript	c.-44-43C>G	intron_variant		NP_003151.2
AURKC	XM_047439253.1 linkuse as main transcript	c.59-43C>G	intron_variant		XP_047295209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AURKC	ENST00000302804.12 linkuse as main transcript	c.59-43C>G		intron_variant		1	NM_001015878.2	ENSP00000302898	A2	Q9UQB9-1

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48041

AN:

150856

Hom.:

8204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.300

GnomAD3 exomes

AF:

0.352

AC:

87351

AN:

248296

Hom.:

16991

AF XY:

0.348

AC XY:

46737

AN XY:

134460

show subpopulations

Gnomad AFR exome

AF:

0.303

Gnomad AMR exome

AF:

0.416

Gnomad ASJ exome

AF:

0.298

Gnomad EAS exome

AF:

0.695

Gnomad SAS exome

AF:

0.368

Gnomad FIN exome

AF:

0.343

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.311

GnomAD4 exome

AF:

0.316

AC:

461440

AN:

1458444

Hom.:

77038

Cov.:

AF XY:

0.317

AC XY:

229796

AN XY:

725678

show subpopulations

Gnomad4 AFR exome

AF:

0.307

Gnomad4 AMR exome

AF:

0.410

Gnomad4 ASJ exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.689

Gnomad4 SAS exome

AF:

0.368

Gnomad4 FIN exome

AF:

0.336

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.331

GnomAD4 genome

AF:

0.319

AC:

48093

AN:

150972

Hom.:

8213

Cov.:

AF XY:

0.323

AC XY:

23815

AN XY:

73698

show subpopulations

Gnomad4 AFR

AF:

0.307

Gnomad4 AMR

AF:

0.352

Gnomad4 ASJ

AF:

0.312

Gnomad4 EAS

AF:

0.685

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.285

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.290

Hom.:

1209

Bravo

AF:

0.322

Asia WGS

AF:

0.484

AC:

1682

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over