NM_024808.5:c.1483-2686A>G

Variant names:

• chr13-72751004-A-G
• rs9564915
• NM_024808.5:c.1483-2686A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024808.5(BORA):​c.1483-2686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,038 control chromosomes in the GnomAD database, including 7,556 homozygotes. 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: 𝑓 0.28 (7556 hom., cov: 31)
• Consequence: BORA NM_024808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 5 publications found

Genes affected

BORA (HGNC:24724): (BORA aurora kinase A activator) BORA is an activator of the protein kinase Aurora A (AURKA; MIM 603072), which is required for centrosome maturation, spindle assembly, and asymmetric protein localization during mitosis (Hutterer et al., 2006 [PubMed 16890155]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BORA	NM_024808.5	c.1483-2686A>G		intron_variant	Intron 10 of 11	ENST00000390667.11	NP_079084.4
BORA	NM_001286746.3	c.1483-2686A>G		intron_variant	Intron 10 of 11		NP_001273675.2
BORA	NM_001366664.2	c.1330-2686A>G		intron_variant	Intron 8 of 9		NP_001353593.1
BORA	NM_001286747.2	c.1273-2686A>G		intron_variant	Intron 9 of 10		NP_001273676.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BORA	ENST00000390667.11	c.1483-2686A>G		intron_variant	Intron 10 of 11	1	NM_024808.5	ENSP00000375082.6

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42950 AN: 151920 Hom.: 7546 Cov.: 31

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.296

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.283 AC: 42973 AN: 152038 Hom.: 7556 Cov.: 31 AF XY: 0.295 AC XY: 21956 AN XY: 74310

African (AFR) AF: 0.0982 AC: 4077 AN: 41500

American (AMR) AF: 0.442 AC: 6744 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2711 AN: 5156

South Asian (SAS) AF: 0.428 AC: 2062 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4408 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21284 AN: 67970

Other (OTH) AF: 0.296 AC: 625 AN: 2112

Alfa AF: 0.300 Hom.: 11867

Bravo AF: 0.276

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.068
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9564915; hg19: chr13-73325142;