rs7047089

chr9-92355698-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.467+9911C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,004 control chromosomes in the GnomAD database, including 17,380 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 0.45 (17380 hom., cov: 32)
• Consequence: CENPP NM_001012267.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CENPP	NM_001012267.3	c.467+9911C>T		intron_variant		ENST00000375587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CENPP	ENST00000375587.8	c.467+9911C>T		intron_variant		1	NM_001012267.3	P1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67740 AN: 151888 Hom.: 17340 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.446 AC: 67826 AN: 152004 Hom.: 17380 Cov.: 32 AF XY: 0.436 AC XY: 32396 AN XY: 74292

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.426

Alfa AF: 0.420 Hom.: 1844

Bravo AF: 0.459

Asia WGS AF: 0.275 AC: 956 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	11
Dann	Benign	0.78

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: rs7047089; hg19: chr9-95117980;