rs11895026

Variant names:

• chr2-24813989-C-A
• rs11895026
• NM_001322101.2:c.217-387C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-24813989-C-A
• chr2-24813989-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322101.2(CENPO):​c.217-387C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,088 control chromosomes in the GnomAD database, including 2,655 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 0.18 (2655 hom., cov: 31)
• Consequence: CENPO NM_001322101.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 12 publications found

Genes affected

CENPO (HGNC:28152): (centromere protein O) This gene encodes a component of the interphase centromere complex. The encoded protein is localized to the centromere throughout the cell cycle and is required for bipolar spindle assembly, chromosome segregation and checkpoint signaling during mitosis. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322101.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPO	NM_001322101.2	MANE Select	c.217-387C>A		intron	N/A	NP_001309030.1	Q9BU64-1
	CENPO	NM_024322.4		c.217-387C>A		intron	N/A	NP_077298.1	Q9BU64-1
	CENPO	NM_001199803.3		c.199-387C>A		intron	N/A	NP_001186732.1	Q9BU64-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPO	ENST00000380834.7	TSL:5 MANE Select	c.217-387C>A		intron	N/A	ENSP00000370214.2	Q9BU64-1
	CENPO	ENST00000260662.2	TSL:1	c.217-387C>A		intron	N/A	ENSP00000260662.1	Q9BU64-1
	CENPO	ENST00000868050.1		c.217-387C>A		intron	N/A	ENSP00000538109.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26725 AN: 151970 Hom.: 2649 Cov.: 31

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.176 AC: 26757 AN: 152088 Hom.: 2655 Cov.: 31 AF XY: 0.175 AC XY: 13000 AN XY: 74350

African (AFR) AF: 0.0894 AC: 3711 AN: 41492

American (AMR) AF: 0.133 AC: 2026 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.119 AC: 617 AN: 5178

South Asian (SAS) AF: 0.132 AC: 635 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2716 AN: 10562

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15466 AN: 67968

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.202 Hom.: 5604

Bravo AF: 0.164

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.49
PhyloP100		-0.0080
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: rs11895026; hg19: chr2-25036858;