dbSNP rs140452971: AURKC:c.-80dupC (chr19-57231163-A-AC) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001015878.2(AURKC):c.-80dupC 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
NM_001015878.2 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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AURKC	NM_001015878.2 link	c.-80dupC	5_prime_UTR_variant	Exon 1 of 7	ENST00000302804.12	NP_001015878.1	Q9UQB9-1
AURKC	XM_047439253.1 link	c.-80dupC	5_prime_UTR_variant	Exon 1 of 5		XP_047295209.1
AURKC	NM_001015879.2 link	c.1+55dupC	intron_variant	Intron 1 of 6		NP_001015879.1	Q9UQB9-3
AURKC	NM_003160.3 link	c.-45+50dupC	intron_variant	Intron 1 of 6		NP_003151.2	Q9UQB9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AURKC	ENST00000302804 link	c.-80dupC		5_prime_UTR_variant	Exon 1 of 7	1	NM_001015878.2	ENSP00000302898.6		Q9UQB9-1

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

GnomAD2 exomes

AF:

0.0103

AC:

1562

AN:

151004

AF XY:

0.00964

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 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

African (AFR)

AF:

0.00406

AC:

128

AN:

31554

American (AMR)

AF:

0.00768

AC:

274

AN:

35686

Ashkenazi Jewish (ASJ)

AF:

0.0000397

AC:

AN:

25160

East Asian (EAS)

AF:

0.127

AC:

4541

AN:

35722

South Asian (SAS)

AF:

0.00321

AC:

254

AN:

79180

European-Finnish (FIN)

AF:

0.0000203

AC:

AN:

49242

Middle Eastern (MID)

AF:

0.000878

AC:

AN:

5694

European-Non Finnish (NFE)

AF:

0.00170

AC:

1826

AN:

1076962

Other (OTH)

AF:

0.00702

AC:

406

AN:

57868

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.554

Heterozygous variant carriers

280

560

841

1121

1401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00687

AC:

1033

AN:

150306

Hom.:

Cov.:

AF XY:

0.00771

AC XY:

565

AN XY:

73322

show subpopulations

African (AFR)

AF:

0.00497

AC:

203

AN:

40846

American (AMR)

AF:

0.0143

AC:

216

AN:

15092

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3450

East Asian (EAS)

AF:

0.0974

AC:

494

AN:

5074

South Asian (SAS)

AF:

0.00337

AC:

AN:

4752

European-Finnish (FIN)

AF:

0.0000974

AC:

AN:

10268

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00138

AC:

AN:

67536

Other (OTH)

AF:

0.00478

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

140

187

234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism (auto)

(source)

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.

rs140452971

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over