Genetic Variant CDCP2:c.1117+107dupC (chr1-54139645-T-TG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001353655.3(CDCP2):c.1117+107dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,534,020 control chromosomes in the GnomAD database, including 25,277 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.27 ( 2569 hom., cov: 28)

Exomes 𝑓: 0.18 ( 22708 hom. )

Consequence

CDCP2
NM_001353655.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.597

Publications

10 publications found

Variant links:

Genes affected

CDCP2 (HGNC:27297): (CUB domain containing protein 2) Predicted to be located in extracellular region. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CDCP2 links:

ENSG00000256407 (HGNC:):

ENSG00000256407 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDCP2	NM_001353655.3 link	c.1117+107dupC		intron_variant	Intron 4 of 5	ENST00000530059.3	NP_001340584.1
CDCP2	NM_201546.5 link	c.1224dupC	p.Met409HisfsTer45	frameshift_variant	Exon 4 of 4		NP_963840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
CDCP2	ENST00000530059.3 link	c.1117+107dupC		intron_variant	Intron 4 of 5	5	NM_001353655.3	ENSP00000489959.1
ENSG00000256407	ENST00000637610.1 link	n.*1281+107dupC		intron_variant	Intron 8 of 9	5		ENSP00000490901.1
CDCP2	ENST00000371330.1 link	c.1224dupC	p.Met409HisfsTer45	frameshift_variant	Exon 4 of 4	2		ENSP00000360381.1
ENSG00000280425	ENST00000623663.2 link	n.1642dupG		non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

27251

AN:

101506

Hom.:

2564

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.292

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.270

GnomAD2 exomes

AF:

0.263

AC:

41098

AN:

156162

AF XY:

0.270

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.316

Gnomad EAS exome

AF:

0.200

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.267

GnomAD4 exome

AF:

0.182

AC:

261014

AN:

1432394

Hom.:

22708

Cov.:

AF XY:

0.184

AC XY:

131048

AN XY:

713048

show subpopulations

African (AFR)

AF:

0.212

AC:

7002

AN:

33068

American (AMR)

AF:

0.0958

AC:

4173

AN:

43552

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

4859

AN:

25536

East Asian (EAS)

AF:

0.167

AC:

6526

AN:

38982

South Asian (SAS)

AF:

0.209

AC:

17712

AN:

84720

European-Finnish (FIN)

AF:

0.134

AC:

7119

AN:

52944

Middle Eastern (MID)

AF:

0.240

AC:

1364

AN:

5672

European-Non Finnish (NFE)

AF:

0.185

AC:

201472

AN:

1088522

Other (OTH)

AF:

0.182

AC:

10787

AN:

59398

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

11209

22419

33628

44838

56047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7116

14232

21348

28464

35580

<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:

0.268

AC:

27282

AN:

101626

Hom.:

2569

Cov.:

AF XY:

0.264

AC XY:

13233

AN XY:

50142

show subpopulations

African (AFR)

AF:

0.246

AC:

8335

AN:

33822

American (AMR)

AF:

0.232

AC:

2103

AN:

9082

Ashkenazi Jewish (ASJ)

AF:

0.292

AC:

619

AN:

2120

East Asian (EAS)

AF:

0.184

AC:

777

AN:

4234

South Asian (SAS)

AF:

0.268

AC:

971

AN:

3624

European-Finnish (FIN)

AF:

0.203

AC:

1391

AN:

6854

Middle Eastern (MID)

AF:

0.279

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.312

AC:

12346

AN:

39592

Other (OTH)

AF:

0.266

AC:

371

AN:

1394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1020

2041

3061

4082

5102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.60

Mutation Taster

=187/13

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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1-54139645-TG-TGG

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