NM_024808.5:c.260+634C>A

Variant names:

• chr13-72732021-C-A
• rs9285280
• NM_024808.5:c.260+634C>A

Variant summary

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

The NM_024808.5(BORA):​c.260+634C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,190 control chromosomes in the GnomAD database, including 61,037 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 0.88 (61037 hom., cov: 32)
• Consequence: BORA NM_024808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024808.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORA	NM_024808.5	MANE Select	c.260+634C>A		intron	N/A	NP_079084.4
	BORA	NM_001286746.3		c.260+634C>A		intron	N/A	NP_001273675.2	Q6PGQ7-1
	BORA	NM_001366664.2		c.153+2928C>A		intron	N/A	NP_001353593.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORA	ENST00000390667.11	TSL:1 MANE Select	c.260+634C>A		intron	N/A	ENSP00000375082.6	Q6PGQ7-1
	BORA	ENST00000613797.4	TSL:1	c.485+634C>A		intron	N/A	ENSP00000479266.1	A0A087WV86
	BORA	ENST00000651477.1		c.260+634C>A		intron	N/A	ENSP00000498664.1	Q6PGQ7-1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133848 AN: 152074 Hom.: 61014 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.880 AC: 133921 AN: 152190 Hom.: 61037 Cov.: 32 AF XY: 0.883 AC XY: 65732 AN XY: 74408

African (AFR) AF: 0.612 AC: 25363 AN: 41432

American (AMR) AF: 0.951 AC: 14561 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3398 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5067 AN: 5180

South Asian (SAS) AF: 0.967 AC: 4663 AN: 4824

European-Finnish (FIN) AF: 0.993 AC: 10543 AN: 10616

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67191 AN: 68042

Other (OTH) AF: 0.920 AC: 1944 AN: 2112

Alfa AF: 0.885 Hom.: 3478

Bravo AF: 0.868

Asia WGS AF: 0.947 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-0.83
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: rs9285280; hg19: chr13-73306159;