rs7047089

Variant names:

• chr9-92355698-C-T
• rs7047089
• NM_001012267.3:c.467+9911C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CENPP	NM_001012267.3	c.467+9911C>T		intron_variant	Intron 4 of 7	ENST00000375587.8	NP_001012267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CENPP	ENST00000375587.8	c.467+9911C>T		intron_variant	Intron 4 of 7	1	NM_001012267.3	ENSP00000364737.3

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

African (AFR) AF: 0.701 AC: 29063 AN: 41486

American (AMR) AF: 0.322 AC: 4917 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3466

East Asian (EAS) AF: 0.151 AC: 781 AN: 5164

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3135 AN: 10552

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25318 AN: 67944

Other (OTH) AF: 0.426 AC: 895 AN: 2102

Alfa AF: 0.433 Hom.: 2056

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
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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: rs7047089; hg19: chr9-95117980;