Genetic Variant NM_001353655.3:c.1117+107delC (chr1-54139645-TG-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_001353655.3(CDCP2):c.1117+107delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,534,560 control chromosomes in the GnomAD database, including 35 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.013 ( 23 hom., cov: 28)

Exomes 𝑓: 0.00099 ( 12 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.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.013 (1318/101698) while in subpopulation AFR AF = 0.0364 (1231/33844). AF 95% confidence interval is 0.0347. There are 23 homozygotes in GnomAd4. There are 667 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 23 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353655.3. 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
	CDCP2	NM_001353655.3	MANE Select	c.1117+107delC		intron	N/A	NP_001340584.1
	CDCP2	NM_201546.5		c.1224delC	p.Met409fs	frameshift	Exon 4 of 4	NP_963840.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CDCP2	ENST00000530059.3	TSL:5 MANE Select	c.1117+107delC		intron	N/A	ENSP00000489959.1
ENSG00000256407	ENST00000637610.1	TSL:5	n.*1281+107delC		intron	N/A	ENSP00000490901.1
CDCP2	ENST00000371330.1	TSL:2	c.1224delC	p.Met409fs	frameshift	Exon 4 of 4	ENSP00000360381.1

Frequencies

GnomAD3 genomes

AF:

0.0129

AC:

1308

AN:

101578

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00672

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000276

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00485

Gnomad NFE

AF:

0.000505

Gnomad OTH

AF:

0.00292

GnomAD2 exomes

AF:

0.00377

AC:

589

AN:

156162

AF XY:

0.00283

show subpopulations

Gnomad AFR exome

AF:

0.0385

Gnomad AMR exome

AF:

0.00345

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000319

Gnomad OTH exome

AF:

0.00190

GnomAD4 exome

AF:

0.000992

AC:

1421

AN:

1432862

Hom.:

Cov.:

AF XY:

0.000831

AC XY:

593

AN XY:

713258

show subpopulations

African (AFR)

AF:

0.0311

AC:

1029

AN:

33086

American (AMR)

AF:

0.00213

AC:

AN:

43608

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25542

East Asian (EAS)

AF:

0.00

AC:

AN:

39052

South Asian (SAS)

AF:

0.0000826

AC:

AN:

84758

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52970

Middle Eastern (MID)

AF:

0.00264

AC:

AN:

5676

European-Non Finnish (NFE)

AF:

0.000126

AC:

137

AN:

1088752

Other (OTH)

AF:

0.00236

AC:

140

AN:

59418

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

174

260

347

434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

160

200

<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:

0.0130

AC:

1318

AN:

101698

Hom.:

Cov.:

AF XY:

0.0133

AC XY:

667

AN XY:

50176

show subpopulations

African (AFR)

AF:

0.0364

AC:

1231

AN:

33844

American (AMR)

AF:

0.00671

AC:

AN:

9088

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2120

East Asian (EAS)

AF:

0.00

AC:

AN:

4236

South Asian (SAS)

AF:

0.000276

AC:

AN:

3628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6866

Middle Eastern (MID)

AF:

0.00526

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.000505

AC:

AN:

39616

Other (OTH)

AF:

0.00287

AC:

AN:

1394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

114

170

227

284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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 v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.60

Mutation Taster

=174/26

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over