rs11576359

Positions:

• chr1-54149893-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001353655.3(CDCP2):​c.79+2951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 152,310 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.035 (142 hom., cov: 32)
• Consequence: CDCP2 NM_001353655.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDCP2	NM_001353655.3	c.79+2951G>A		intron_variant		ENST00000530059.3	NP_001340584.1
CDCP2	NM_201546.5	c.79+2951G>A		intron_variant			NP_963840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDCP2	ENST00000530059.3	c.79+2951G>A		intron_variant		5	NM_001353655.3	ENSP00000489959	P1
CDCP2	ENST00000371330.1	c.79+2951G>A		intron_variant		2		ENSP00000360381

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5282 AN: 152192 Hom.: 140 Cov.: 32

Gnomad AFR AF: 0.00914

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0349

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0347 AC: 5291 AN: 152310 Hom.: 142 Cov.: 32 AF XY: 0.0362 AC XY: 2694 AN XY: 74480

Gnomad4 AFR AF: 0.00911

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.0233

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0545

Gnomad4 NFE AF: 0.0381

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0397 Hom.: 41

Bravo AF: 0.0358

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.57

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

LitVar

Other links and lift over

dbSNP: rs11576359; hg19: chr1-54615566;