chr17-8209868-A-T

Variant names:

• chr17-8209868-A-T
• rs3027260
• NM_004217.4:c.48+309T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004217.4(AURKB):​c.48+309T>A variant causes a intron 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AURKB NM_004217.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 8 publications found

Genes affected

AURKB (HGNC:11390): (aurora kinase B) This gene encodes a member of the aurora kinase subfamily of serine/threonine kinases. The genes encoding the other two members of this subfamily are located on chromosomes 19 and 20. These kinases participate in the regulation of alignment and segregation of chromosomes during mitosis and meiosis through association with microtubules. A pseudogene of this gene is located on chromosome 8. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AURKB	NM_004217.4	c.48+309T>A		intron_variant	Intron 2 of 8	ENST00000585124.6	NP_004208.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AURKB	ENST00000585124.6	c.48+309T>A		intron_variant	Intron 2 of 8	1	NM_004217.4	ENSP00000463999.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 312766 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 162240

African (AFR) AF: 0.00 AC: 0 AN: 7276

American (AMR) AF: 0.00 AC: 0 AN: 9030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10410

East Asian (EAS) AF: 0.00 AC: 0 AN: 20408

South Asian (SAS) AF: 0.00 AC: 0 AN: 25854

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23252

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1518

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 195708

Other (OTH) AF: 0.00 AC: 0 AN: 19310

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 85887

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		0.30
PromoterAI		0.028	Neutral

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: rs3027260; hg19: chr17-8113186;