rs3841798

Positions:

• chr1-54139645-TG-T
• chr1-54139645-TG-TGG
• chr1-54139645-TG-TGGG
• chr1-54139645-TG-TGGGG
• chr1-54139645-TG-TGGGGG

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BS1 BS2

The NM_201546.5(CDCP2):​c.1224delC​(p.Met409fs) variant causes a frameshift 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. Variant has been reported in Lovd as Benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P408P) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.013 (23 hom., cov: 28)
  • Exomes 𝑓: 0.00099 (12 hom.)
• Consequence: CDCP2 NM_201546.5 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

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]

ENSG00000256407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 1-54139645-TG-T is Benign according to our data. Variant chr1-54139645-TG-T is described in Lovd as [Benign].
• 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 male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 23 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDCP2	NM_001353655.3	c.1117+107delC		intron_variant		ENST00000530059.3	NP_001340584.1
CDCP2	NM_201546.5	c.1224delC	p.Met409fs	frameshift_variant	4/4		NP_963840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDCP2	ENST00000530059.3	c.1117+107delC		intron_variant		5	NM_001353655.3	ENSP00000489959.1
ENSG00000256407	ENST00000637610.1	n.*1281+107delC		intron_variant		5		ENSP00000490901.1
CDCP2	ENST00000371330.1	c.1224delC	p.Met409fs	frameshift_variant	4/4	2		ENSP00000360381.1
ENSG00000280425	ENST00000623663.2	n.1642delG		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.0129 AC: 1308 AN: 101578 Hom.: 23 Cov.: 28

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

GnomAD3 exomes AF: 0.00377 AC: 589 AN: 156162 Hom.: 3 AF XY: 0.00283 AC XY: 241 AN XY: 85076

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 SAS 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.: 12 Cov.: 59 AF XY: 0.000831 AC XY: 593 AN XY: 713258

Gnomad4 AFR exome AF: 0.0311

Gnomad4 AMR exome AF: 0.00213

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000826

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000126

Gnomad4 OTH exome AF: 0.00236

GnomAD4 genome AF: 0.0130 AC: 1318 AN: 101698 Hom.: 23 Cov.: 28 AF XY: 0.0133 AC XY: 667 AN XY: 50176

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.00671

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000276

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000505

Gnomad4 OTH AF: 0.00287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs3841798; hg19: chr1-54605318;