NM_001211.6:c.2678+1568T>G

Variant names:

• chr15-40215042-T-G
• rs7182070
• NM_001211.6:c.2678+1568T>G

Variant summary

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

The NM_001211.6(BUB1B):​c.2678+1568T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,146 control chromosomes in the GnomAD database, including 1,737 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 0.14 (1737 hom., cov: 30)
• Consequence: BUB1B NM_001211.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

BUB1B (HGNC:1149): (BUB1 mitotic checkpoint serine/threonine kinase B) This gene encodes a kinase involved in spindle checkpoint function. The protein has been localized to the kinetochore and plays a role in the inhibition of the anaphase-promoting complex/cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. Impaired spindle checkpoint function has been found in many forms of cancer. [provided by RefSeq, Jul 2008]

LOC107984763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BUB1B	NM_001211.6	c.2678+1568T>G		intron_variant	Intron 20 of 22	ENST00000287598.11	NP_001202.5
LOC107984763	XR_001751506.2	n.217+24443A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BUB1B	ENST00000287598.11	c.2678+1568T>G		intron_variant	Intron 20 of 22	1	NM_001211.6	ENSP00000287598.7
BUB1B	ENST00000412359.7	c.2720+1568T>G		intron_variant	Intron 20 of 22	2		ENSP00000398470.3

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21936 AN: 152028 Hom.: 1734 Cov.: 30

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.144 AC: 21953 AN: 152146 Hom.: 1737 Cov.: 30 AF XY: 0.143 AC XY: 10615 AN XY: 74382

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0618

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0888 Hom.: 121

Bravo AF: 0.141

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.68

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: rs7182070; hg19: chr15-40507243;