Variant 19-57231146-G-GC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The ENST00000302804.12(AURKC):c.-99dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 1,488,986 control chromosomes in the GnomAD database, including 196,064 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.46 ( 16849 hom., cov: 0)

Exomes 𝑓: 0.50 ( 179215 hom. )

Consequence

AURKC
ENST00000302804.12 5_prime_UTR

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: -0.0610

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 -9 ACMG points.

BP6

Variant 19-57231146-G-GC is Benign according to our data. Variant chr19-57231146-G-GC is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 330226.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1, Likely_benign=2}.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
AURKC	NM_001015878.2 linkuse as main transcript	c.-99dup	5_prime_UTR_variant	1/7	ENST00000302804.12	NP_001015878.1
AURKC	XM_047439253.1 linkuse as main transcript	c.-99dup	5_prime_UTR_variant	1/5		XP_047295209.1
AURKC	NM_001015879.2 linkuse as main transcript	c.1+36dup	intron_variant			NP_001015879.1
AURKC	NM_003160.3 linkuse as main transcript	c.-45+31dup	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.-99dup	5_prime_UTR_variant	1/7	1	NM_001015878.2	ENSP00000302898	A2	Q9UQB9-1
AURKC	ENST00000415300.6 linkuse as main transcript	c.1+36dup	intron_variant		1		ENSP00000407162		Q9UQB9-3
AURKC	ENST00000601799.5 linkuse as main transcript	c.-99dup	5_prime_UTR_variant, NMD_transcript_variant	1/6	3		ENSP00000468918

Frequencies

GnomAD3 genomes

AF:

0.460

AC:

69547

AN:

151246

Hom.:

16846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.528

Gnomad OTH

AF:

0.454

GnomAD3 exomes

AF:

0.373

AC:

46709

AN:

125078

Hom.:

15424

AF XY:

0.385

AC XY:

25650

AN XY:

66628

show subpopulations

Gnomad AFR exome

AF:

0.200

Gnomad AMR exome

AF:

0.319

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.0787

Gnomad SAS exome

AF:

0.428

Gnomad FIN exome

AF:

0.515

Gnomad NFE exome

AF:

0.409

Gnomad OTH exome

AF:

0.377

GnomAD4 exome

AF:

0.502

AC:

671249

AN:

1337622

Hom.:

179215

Cov.:

AF XY:

0.503

AC XY:

331967

AN XY:

659638

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.427

Gnomad4 ASJ exome

AF:

0.544

Gnomad4 EAS exome

AF:

0.151

Gnomad4 SAS exome

AF:

0.505

Gnomad4 FIN exome

AF:

0.548

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.476

GnomAD4 genome

AF:

0.460

AC:

69567

AN:

151364

Hom.:

16849

Cov.:

AF XY:

0.459

AC XY:

33953

AN XY:

73914

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.528

Gnomad4 OTH

AF:

0.456

Alfa

AF:

0.145

Hom.:

606

Asia WGS

AF:

0.339

AC:

1176

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Spermatogenic Failure

Uncertain:1Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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