rs10761156

Positions:

• chr9-92409570-C-T

Variant summary

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

The NM_001012267.3(CENPP):​c.564+29711C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,110 control chromosomes in the GnomAD database, including 15,750 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 0.42 (15750 hom., cov: 32)
• Consequence: CENPP NM_001012267.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CENPP	NM_001012267.3	c.564+29711C>T		intron_variant		ENST00000375587.8	NP_001012267.1
CENPP	NM_001286969.1	c.228+29711C>T		intron_variant			NP_001273898.1
CENPP	XM_011518689.2	c.564+29711C>T		intron_variant			XP_011516991.1
CENPP	XM_024447543.2	c.288+29711C>T		intron_variant			XP_024303311.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CENPP	ENST00000375587.8	c.564+29711C>T		intron_variant		1	NM_001012267.3	ENSP00000364737	P1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63263 AN: 151992 Hom.: 15743 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.416 AC: 63271 AN: 152110 Hom.: 15750 Cov.: 32 AF XY: 0.422 AC XY: 31351 AN XY: 74336

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.448

Alfa AF: 0.491 Hom.: 17751

Bravo AF: 0.404

Asia WGS AF: 0.601 AC: 2087 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.70

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: rs10761156; hg19: chr9-95171852;