rs4885035

chr13-72732294-A-Cchr13-72732294-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024808.5(BORA):c.260+907A>C 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 152,136 control chromosomes in the GnomAD database, including 60,982 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 (60982 hom., cov: 31)
• Consequence: BORA NM_024808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BORA	NM_024808.5	c.260+907A>C		intron_variant		ENST00000390667.11
BORA	NM_001286746.3	c.260+907A>C		intron_variant
BORA	NM_001286747.2	c.51-2666A>C		intron_variant
BORA	NM_001366664.2	c.153+3201A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BORA	ENST00000390667.11	c.260+907A>C		intron_variant		1	NM_024808.5	P1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133751 AN: 152018 Hom.: 60959 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.880 AC: 133825 AN: 152136 Hom.: 60982 Cov.: 31 AF XY: 0.883 AC XY: 65684 AN XY: 74386

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.918

Alfa AF: 0.921 Hom.: 8205

Bravo AF: 0.868

Asia WGS AF: 0.947 AC: 3292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	6.7
Dann	Benign	0.63

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

Other links and lift over

dbSNP: rs4885035; hg19: chr13-73306432;