Variant 19-57231163-A-AC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000302804.12(AURKC):c.-80dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00547 in 1,547,374 control chromosomes in the GnomAD database, including 373 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0069 ( 41 hom., cov: 30)

Exomes 𝑓: 0.0053 ( 332 hom. )

Consequence

AURKC
ENST00000302804.12 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00400

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 -10 ACMG points.

BP6

Variant 19-57231163-A-AC is Benign according to our data. Variant chr19-57231163-A-AC is described in ClinVar as [Likely_benign]. Clinvar id is 330227.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
AURKC	NM_001015878.2 linkuse as main transcript	c.-80dup	5_prime_UTR_variant	1/7	ENST00000302804.12	NP_001015878.1
AURKC	XM_047439253.1 linkuse as main transcript	c.-80dup	5_prime_UTR_variant	1/5		XP_047295209.1
AURKC	NM_001015879.2 linkuse as main transcript	c.1+55dup	intron_variant			NP_001015879.1
AURKC	NM_003160.3 linkuse as main transcript	c.-45+50dup	intron_variant			NP_003151.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AURKC	ENST00000302804.12 linkuse as main transcript	c.-80dup	5_prime_UTR_variant	1/7	1	NM_001015878.2	ENSP00000302898	A2	Q9UQB9-1
AURKC	ENST00000415300.6 linkuse as main transcript	c.1+55dup	intron_variant		1		ENSP00000407162		Q9UQB9-3
AURKC	ENST00000601799.5 linkuse as main transcript	c.-80dup	5_prime_UTR_variant, NMD_transcript_variant	1/6	3		ENSP00000468918

Frequencies

GnomAD3 genomes

AF:

0.00690

AC:

1037

AN:

150184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00499

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0979

Gnomad SAS

AF:

0.00336

Gnomad FIN

AF:

0.0000974

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00138

Gnomad OTH

AF:

0.00484

GnomAD3 exomes

AF:

0.0103

AC:

1562

AN:

151004

Hom.:

176

AF XY:

0.00964

AC XY:

768

AN XY:

79708

show subpopulations

Gnomad AFR exome

AF:

0.00385

Gnomad AMR exome

AF:

0.00894

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.102

Gnomad SAS exome

AF:

0.00262

Gnomad FIN exome

AF:

0.000132

Gnomad NFE exome

AF:

0.00143

Gnomad OTH exome

AF:

0.00769

GnomAD4 exome

AF:

0.00532

AC:

7436

AN:

1397068

Hom.:

332

Cov.:

AF XY:

0.00525

AC XY:

3620

AN XY:

689048

show subpopulations

Gnomad4 AFR exome

AF:

0.00406

Gnomad4 AMR exome

AF:

0.00768

Gnomad4 ASJ exome

AF:

0.0000397

Gnomad4 EAS exome

AF:

0.127

Gnomad4 SAS exome

AF:

0.00321

Gnomad4 FIN exome

AF:

0.0000203

Gnomad4 NFE exome

AF:

0.00170

Gnomad4 OTH exome

AF:

0.00702

GnomAD4 genome

AF:

0.00687

AC:

1033

AN:

150306

Hom.:

Cov.:

AF XY:

0.00771

AC XY:

565

AN XY:

73322

show subpopulations

Gnomad4 AFR

AF:

0.00497

Gnomad4 AMR

AF:

0.0143

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0974

Gnomad4 SAS

AF:

0.00337

Gnomad4 FIN

AF:

0.0000974

Gnomad4 NFE

AF:

0.00138

Gnomad4 OTH

AF:

0.00478

Alfa

AF:

0.000914

Hom.:

Asia WGS

AF:

0.0370

AC:

128

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Spermatogenic Failure

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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