ENST00000506882.5:n.*19A>G – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000506882.5(CENPC):n.*19A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 455,750 control chromosomes in the GnomAD database, including 94,518 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 0.63 ( 30445 hom., cov: 32)

Exomes 𝑓: 0.64 ( 64073 hom. )

Consequence

CENPC
ENST00000506882.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.90

Publications

6 publications found

Variant links:

Genes affected

CENPC (HGNC:1854): (centromere protein C) Centromere protein C 1 is a centromere autoantigen and a component of the inner kinetochore plate. The protein is required for maintaining proper kinetochore size and a timely transition to anaphase. A putative pseudogene exists on chromosome 12. [provided by RefSeq, Jul 2008]

CENPC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPC	NM_001812.4 link	c.1612+1412A>G		intron_variant	Intron 9 of 18	ENST00000273853.11	NP_001803.2	Q03188-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CENPC	ENST00000273853.11 link	c.1612+1412A>G		intron_variant	Intron 9 of 18	1	NM_001812.4	ENSP00000273853.6		Q03188-1

Frequencies

GnomAD3 genomes

AF:

0.630

AC:

95690

AN:

151866

Hom.:

30398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.733

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.813

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.732

Gnomad NFE

AF:

0.598

Gnomad OTH

AF:

0.670

GnomAD2 exomes

AF:

0.675

AC:

86475

AN:

128164

AF XY:

0.668

show subpopulations

Gnomad AFR exome

AF:

0.632

Gnomad AMR exome

AF:

0.795

Gnomad ASJ exome

AF:

0.648

Gnomad EAS exome

AF:

0.819

Gnomad FIN exome

AF:

0.566

Gnomad NFE exome

AF:

0.603

Gnomad OTH exome

AF:

0.660

GnomAD4 exome

AF:

0.645

AC:

195800

AN:

303766

Hom.:

64073

Cov.:

AF XY:

0.646

AC XY:

111648

AN XY:

172954

show subpopulations

African (AFR)

AF:

0.638

AC:

5498

AN:

8618

American (AMR)

AF:

0.795

AC:

21697

AN:

27280

Ashkenazi Jewish (ASJ)

AF:

0.646

AC:

6964

AN:

10784

East Asian (EAS)

AF:

0.812

AC:

7474

AN:

9208

South Asian (SAS)

AF:

0.677

AC:

40432

AN:

59684

European-Finnish (FIN)

AF:

0.571

AC:

7064

AN:

12362

Middle Eastern (MID)

AF:

0.732

AC:

2034

AN:

2778

European-Non Finnish (NFE)

AF:

0.601

AC:

95503

AN:

158828

Other (OTH)

AF:

0.642

AC:

9134

AN:

14224

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

3791

7583

11374

15166

18957

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

592

1184

1776

2368

2960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.630

AC:

95785

AN:

151984

Hom.:

30445

Cov.:

AF XY:

0.635

AC XY:

47170

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.630

AC:

26098

AN:

41440

American (AMR)

AF:

0.733

AC:

11180

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2186

AN:

3466

East Asian (EAS)

AF:

0.813

AC:

4205

AN:

5174

South Asian (SAS)

AF:

0.698

AC:

3365

AN:

4820

European-Finnish (FIN)

AF:

0.568

AC:

6005

AN:

10572

Middle Eastern (MID)

AF:

0.729

AC:

213

AN:

292

European-Non Finnish (NFE)

AF:

0.598

AC:

40611

AN:

67952

Other (OTH)

AF:

0.673

AC:

1422

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1807

3613

5420

7226

9033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

780

1560

2340

3120

3900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.613

Hom.:

16811

Bravo

AF:

0.645

Asia WGS

AF:

0.771

AC:

2679

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

(source)

DANN

Benign

0.39

PhyloP100

-1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over