rs58264281

Positions:

• chr19-57231121-C-A
• chr19-57231121-C-G
• chr19-57231121-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001015878.2(AURKC):​c.-128C>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: AURKC NM_001015878.2 5_prime_UTR_premature_start_codon_gain
• Scores: Splicing: ADA: 0.00001267
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AURKC	NM_001015878.2	c.-128C>A		5_prime_UTR_premature_start_codon_gain_variant	1/7	ENST00000302804.12	NP_001015878.1
AURKC	NM_001015878.2	c.-128C>A		5_prime_UTR_variant	1/7	ENST00000302804.12	NP_001015878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AURKC	ENST00000302804	c.-128C>A		5_prime_UTR_premature_start_codon_gain_variant	1/7	1	NM_001015878.2	ENSP00000302898.6
AURKC	ENST00000302804	c.-128C>A		5_prime_UTR_variant	1/7	1	NM_001015878.2	ENSP00000302898.6
AURKC	ENST00000415300.6	c.1+7C>A		splice_region_variant, intron_variant		1		ENSP00000407162.1
AURKC	ENST00000601799.5	n.-128C>A		upstream_gene_variant		3		ENSP00000468918.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 42

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000013
dbscSNV1_RF	Benign	0.0080
SpliceAI score (max)		0.050		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

Other links and lift over

dbSNP: rs58264281; hg19: chr19-57742489;