Genetic Variant CDCP2:c.1117+107_1117+108insGC (chr1-54139645-T-TGC) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_201546.5(CDCP2):c.1224_1225insGC(p.Met409AlafsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00384 in 1,534,478 control chromosomes in the GnomAD database, including 20 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 1 hom., cov: 28)

Exomes 𝑓: 0.0037 ( 19 hom. )

Consequence

CDCP2
NM_201546.5 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.597

Publications

0 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: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 1-54139645-T-TGC is Benign according to our data. Variant chr1-54139645-T-TGC is described in ClinVar as Likely_benign. ClinVar VariationId is 2638827.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 19 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201546.5. 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
	CDCP2	NM_001353655.3	MANE Select	c.1117+107_1117+108insGC		intron	N/A	NP_001340584.1	Q5VXM1-3
	CDCP2	NM_201546.5		c.1224_1225insGC	p.Met409AlafsTer2	frameshift	Exon 4 of 4	NP_963840.2	Q5VXM1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CDCP2	ENST00000530059.3	TSL:5 MANE Select	c.1117+107_1117+108insGC		intron	N/A	ENSP00000489959.1	Q5VXM1-3
ENSG00000256407	ENST00000637610.1	TSL:5	n.1281+107_1281+108insGC		intron	N/A	ENSP00000490901.1	A0A1B0GWF0
CDCP2	ENST00000371330.1	TSL:2	c.1224_1225insGC	p.Met409AlafsTer2	frameshift	Exon 4 of 4	ENSP00000360381.1	Q5VXM1-1

Frequencies

GnomAD3 genomes

AF:

0.00521

AC:

529

AN:

101576

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.00661

Gnomad ASJ

AF:

0.0113

Gnomad EAS

AF:

0.000235

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.000437

Gnomad MID

AF:

0.0146

Gnomad NFE

AF:

0.00833

Gnomad OTH

AF:

0.00438

GnomAD2 exomes

AF:

0.00524

AC:

818

AN:

156162

AF XY:

0.00563

show subpopulations

Gnomad AFR exome

AF:

0.00124

Gnomad AMR exome

AF:

0.00543

Gnomad ASJ exome

AF:

0.00991

Gnomad EAS exome

AF:

0.0000727

Gnomad FIN exome

AF:

0.0000762

Gnomad NFE exome

AF:

0.00862

Gnomad OTH exome

AF:

0.00815

GnomAD4 exome

AF:

0.00374

AC:

5357

AN:

1432782

Hom.:

Cov.:

AF XY:

0.00374

AC XY:

2671

AN XY:

713226

show subpopulations

African (AFR)

AF:

0.00133

AC:

AN:

33088

American (AMR)

AF:

0.00300

AC:

131

AN:

43606

Ashkenazi Jewish (ASJ)

AF:

0.00595

AC:

152

AN:

25542

East Asian (EAS)

AF:

0.0000256

AC:

AN:

39052

South Asian (SAS)

AF:

0.00142

AC:

120

AN:

84758

European-Finnish (FIN)

AF:

0.000227

AC:

AN:

52898

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

5676

European-Non Finnish (NFE)

AF:

0.00421

AC:

4582

AN:

1088744

Other (OTH)

AF:

0.00409

AC:

243

AN:

59418

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

304

608

912

1216

1520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

168

336

504

672

840

<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:

0.00519

AC:

528

AN:

101696

Hom.:

Cov.:

AF XY:

0.00456

AC XY:

229

AN XY:

50176

show subpopulations

African (AFR)

AF:

0.00157

AC:

AN:

33844

American (AMR)

AF:

0.00660

AC:

AN:

9088

Ashkenazi Jewish (ASJ)

AF:

0.0113

AC:

AN:

2120

East Asian (EAS)

AF:

0.000236

AC:

AN:

4236

South Asian (SAS)

AF:

0.00248

AC:

AN:

3628

European-Finnish (FIN)

AF:

0.000437

AC:

AN:

6866

Middle Eastern (MID)

AF:

0.0105

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.00833

AC:

330

AN:

39616

Other (OTH)

AF:

0.00431

AC:

AN:

1392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

106

132

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.60

Mutation Taster

=197/3

polymorphism

(source)

Splicing

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