chr1-54139645-TG-T

Position:

• chr1-54139645-TG-T

Variant summary

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

The NM_001353655.3(CDCP2):​c.1117+107del 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. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.013 (23 hom., cov: 28)
  • Exomes 𝑓: 0.00099 (12 hom.)
• Consequence: CDCP2 NM_001353655.3 intron
• 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]

(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	UniProt
CDCP2	NM_001353655.3	c.1117+107del		intron_variant		ENST00000530059.3
CDCP2	NM_201546.5	c.1224del	p.Met409Ter	frameshift_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDCP2	ENST00000530059.3	c.1117+107del		intron_variant		5	NM_001353655.3	P1
	ENST00000623663.2	n.1642del		non_coding_transcript_exon_variant	2/2	5
CDCP2	ENST00000371330.1	c.1224del	p.Met409Ter	frameshift_variant	4/4	2

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;