19-57231966-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000302804.12(AURKC):​c.105-67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 1,604,894 control chromosomes in the GnomAD database, including 83,949 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7978 hom., cov: 31)
Exomes 𝑓: 0.31 ( 75971 hom. )

Consequence

AURKC
ENST00000302804.12 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -1.32
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]

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=-0.92).
BP6
Variant 19-57231966-C-T is Benign according to our data. Variant chr19-57231966-C-T is described in ClinVar as [Benign]. Clinvar id is 1248562.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AURKCNM_001015878.2 linkuse as main transcriptc.105-67C>T intron_variant ENST00000302804.12 NP_001015878.1
AURKCNM_001015879.2 linkuse as main transcriptc.48-67C>T intron_variant NP_001015879.1
AURKCNM_003160.3 linkuse as main transcriptc.3-67C>T intron_variant NP_003151.2
AURKCXM_047439253.1 linkuse as main transcriptc.105-67C>T intron_variant XP_047295209.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AURKCENST00000302804.12 linkuse as main transcriptc.105-67C>T intron_variant 1 NM_001015878.2 ENSP00000302898 A2Q9UQB9-1

Frequencies

GnomAD3 genomes
AF:
0.312
AC:
47276
AN:
151740
Hom.:
7970
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.282
Gnomad AMI
AF:
0.155
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.314
Gnomad EAS
AF:
0.683
Gnomad SAS
AF:
0.367
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.261
Gnomad NFE
AF:
0.285
Gnomad OTH
AF:
0.296
GnomAD4 exome
AF:
0.315
AC:
457380
AN:
1453034
Hom.:
75971
Cov.:
32
AF XY:
0.315
AC XY:
227747
AN XY:
723436
show subpopulations
Gnomad4 AFR exome
AF:
0.280
Gnomad4 AMR exome
AF:
0.408
Gnomad4 ASJ exome
AF:
0.306
Gnomad4 EAS exome
AF:
0.687
Gnomad4 SAS exome
AF:
0.354
Gnomad4 FIN exome
AF:
0.340
Gnomad4 NFE exome
AF:
0.294
Gnomad4 OTH exome
AF:
0.329
GnomAD4 genome
AF:
0.312
AC:
47325
AN:
151860
Hom.:
7978
Cov.:
31
AF XY:
0.317
AC XY:
23520
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.282
Gnomad4 AMR
AF:
0.350
Gnomad4 ASJ
AF:
0.314
Gnomad4 EAS
AF:
0.684
Gnomad4 SAS
AF:
0.366
Gnomad4 FIN
AF:
0.356
Gnomad4 NFE
AF:
0.285
Gnomad4 OTH
AF:
0.293
Alfa
AF:
0.290
Hom.:
11993
Bravo
AF:
0.313
Asia WGS
AF:
0.475
AC:
1650
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 submitterclinical testingGeneDxNov 10, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.13
DANN
Benign
0.59

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.

Other links and lift over

dbSNP: rs758099; hg19: chr19-57743334; COSMIC: COSV57138836; COSMIC: COSV57138836; API