Variant chr19-57231125-AGGACGAGCAGGATT-A 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.-120_-107del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 1,456,290 control chromosomes in the GnomAD database, including 509,731 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44830 hom., cov: 0)

Exomes 𝑓: 0.84 ( 464901 hom. )

Consequence

AURKC
ENST00000302804.12 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.896

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 19-57231125-AGGACGAGCAGGATT-A is Benign according to our data. Variant chr19-57231125-AGGACGAGCAGGATT-A is described in ClinVar as [Benign]. Clinvar id is 1295147.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
AURKC	NM_001015878.2 linkuse as main transcript	c.-120_-107del	5_prime_UTR_variant	1/7	ENST00000302804.12	NP_001015878.1
AURKC	XM_047439253.1 linkuse as main transcript	c.-120_-107del	5_prime_UTR_variant	1/5		XP_047295209.1
AURKC	NM_001015879.2 linkuse as main transcript	c.1+15_1+28del	intron_variant			NP_001015879.1
AURKC	NM_003160.3 linkuse as main transcript	c.-45+10_-45+23del	splice_region_variant, 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.-120_-107del	5_prime_UTR_variant	1/7	1	NM_001015878.2	ENSP00000302898	A2	Q9UQB9-1
AURKC	ENST00000415300.6 linkuse as main transcript	c.1+15_1+28del	intron_variant		1		ENSP00000407162		Q9UQB9-3
AURKC	ENST00000601799.5 linkuse as main transcript		upstream_gene_variant		3		ENSP00000468918

Frequencies

GnomAD3 genomes

AF:

0.762

AC:

115317

AN:

151364

Hom.:

44821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.805

Gnomad AMR

AF:

0.792

Gnomad ASJ

AF:

0.855

Gnomad EAS

AF:

0.846

Gnomad SAS

AF:

0.852

Gnomad FIN

AF:

0.906

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.815

Gnomad OTH

AF:

0.745

GnomAD3 exomes

AF:

0.824

AC:

107947

AN:

131070

Hom.:

50722

AF XY:

0.831

AC XY:

57470

AN XY:

69170

show subpopulations

Gnomad AFR exome

AF:

0.550

Gnomad AMR exome

AF:

0.842

Gnomad ASJ exome

AF:

0.854

Gnomad EAS exome

AF:

0.856

Gnomad SAS exome

AF:

0.872

Gnomad FIN exome

AF:

0.926

Gnomad NFE exome

AF:

0.797

Gnomad OTH exome

AF:

0.797

GnomAD4 exome

AF:

0.835

AC:

1089902

AN:

1304810

Hom.:

464901

AF XY:

0.838

AC XY:

538365

AN XY:

642606

show subpopulations

Gnomad4 AFR exome

AF:

0.599

Gnomad4 AMR exome

AF:

0.853

Gnomad4 ASJ exome

AF:

0.872

Gnomad4 EAS exome

AF:

0.842

Gnomad4 SAS exome

AF:

0.881

Gnomad4 FIN exome

AF:

0.901

Gnomad4 NFE exome

AF:

0.835

Gnomad4 OTH exome

AF:

0.821

GnomAD4 genome

AF:

0.762

AC:

115364

AN:

151480

Hom.:

44830

Cov.:

AF XY:

0.768

AC XY:

56818

AN XY:

74000

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.792

Gnomad4 ASJ

AF:

0.855

Gnomad4 EAS

AF:

0.847

Gnomad4 SAS

AF:

0.850

Gnomad4 FIN

AF:

0.906

Gnomad4 NFE

AF:

0.815

Gnomad4 OTH

AF:

0.744

Alfa

AF:

0.776

Hom.:

8074

Asia WGS

AF:

0.806

AC:

2797

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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