chr16-81031097-G-A

Variant names:

• chr16-81031097-G-A
• rs1048194
• NM_001100624.3:c.*2446G>A

Variant summary

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

The NM_001100624.3(CENPN):​c.*2446G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 151,530 control chromosomes in the GnomAD database, including 498 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 0.080 (498 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CENPN NM_001100624.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 18 publications found

Genes affected

CENPN (HGNC:30873): (centromere protein N) The protein encoded by this gene forms part of the nucleosome-associated complex and is important for kinetochore assembly. It is bound to kinetochores during S phase and G2 and recruits other proteins to the centromere. Pseudogenes of this gene are located on chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ENSG00000284512 (HGNC:):

CENPN-AS1 (HGNC:55106): (CENPN antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100624.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPN	NM_001100624.3	MANE Select	c.*2446G>A		3_prime_UTR	Exon 11 of 11	NP_001094094.2
	CENPN	NM_001270473.2		c.*2446G>A		3_prime_UTR	Exon 10 of 10	NP_001257402.1
	CENPN	NM_001270474.2		c.*2446G>A		3_prime_UTR	Exon 10 of 10	NP_001257403.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPN	ENST00000305850.10	TSL:1 MANE Select	c.*2446G>A		3_prime_UTR	Exon 11 of 11	ENSP00000305608.5
	ENSG00000284512	ENST00000640345.1	TSL:5	c.*2+3658C>T		intron	N/A	ENSP00000492798.1
	ENSG00000261061	ENST00000566639.1	TSL:6	n.328G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12087 AN: 151412 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0262

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0670

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0799 AC: 12105 AN: 151530 Hom.: 498 Cov.: 32 AF XY: 0.0785 AC XY: 5813 AN XY: 74010

African (AFR) AF: 0.111 AC: 4578 AN: 41258

American (AMR) AF: 0.0504 AC: 767 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0254 AC: 122 AN: 4800

European-Finnish (FIN) AF: 0.105 AC: 1092 AN: 10406

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5216 AN: 67886

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0621 Hom.: 96

Bravo AF: 0.0771

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.66
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1048194; hg19: chr16-81064702;