Variant 19-57231335-A-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.58+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,550,982 control chromosomes in the GnomAD database, including 82,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8529 hom., cov: 30)

Exomes 𝑓: 0.32 ( 73838 hom. )

Consequence

AURKC
ENST00000302804.12 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.807

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 19-57231335-A-G is Benign according to our data. Variant chr19-57231335-A-G is described in ClinVar as [Benign]. Clinvar id is 1257509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
AURKC	NM_001015878.2 linkuse as main transcript	c.58+29A>G	intron_variant	ENST00000302804.12	NP_001015878.1
AURKC	NM_001015879.2 linkuse as main transcript	c.1+221A>G	intron_variant		NP_001015879.1
AURKC	NM_003160.3 linkuse as main transcript	c.-45+216A>G	intron_variant		NP_003151.2
AURKC	XM_047439253.1 linkuse as main transcript	c.58+29A>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.58+29A>G		intron_variant		1	NM_001015878.2	ENSP00000302898	A2	Q9UQB9-1
AURKC	ENST00000415300.6 linkuse as main transcript	c.1+221A>G		intron_variant		1		ENSP00000407162		Q9UQB9-3
AURKC	ENST00000599062.5 linkuse as main transcript	c.58+29A>G		intron_variant		1		ENSP00000469983	P2
AURKC	ENST00000601799.5 linkuse as main transcript	c.87A>G	p.Ala29=	synonymous_variant, NMD_transcript_variant	1/6	3		ENSP00000468918

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49149

AN:

151704

Hom.:

8520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.688

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.303

GnomAD3 exomes

AF:

0.358

AC:

55261

AN:

154544

Hom.:

10865

AF XY:

0.353

AC XY:

28807

AN XY:

81522

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.410

Gnomad ASJ exome

AF:

0.302

Gnomad EAS exome

AF:

0.693

Gnomad SAS exome

AF:

0.357

Gnomad FIN exome

AF:

0.348

Gnomad NFE exome

AF:

0.291

Gnomad OTH exome

AF:

0.313

GnomAD4 exome

AF:

0.317

AC:

443307

AN:

1399160

Hom.:

73838

Cov.:

AF XY:

0.317

AC XY:

218719

AN XY:

690158

show subpopulations

Gnomad4 AFR exome

AF:

0.320

Gnomad4 AMR exome

AF:

0.407

Gnomad4 ASJ exome

AF:

0.306

Gnomad4 EAS exome

AF:

0.689

Gnomad4 SAS exome

AF:

0.357

Gnomad4 FIN exome

AF:

0.340

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.335

GnomAD4 genome

AF:

0.324

AC:

49205

AN:

151822

Hom.:

8529

Cov.:

AF XY:

0.329

AC XY:

24387

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.320

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.312

Gnomad4 EAS

AF:

0.689

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.357

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.300

Alfa

AF:

0.255

Hom.:

1496

Bravo

AF:

0.327

Asia WGS

AF:

0.483

AC:

1678

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	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.78

DANN

Benign

0.32

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

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