rs2952556

chr7-121287738-G-A

Variant summary

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

The NM_024913.5(CPED1):c.2869-7702G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,988 control chromosomes in the GnomAD database, including 18,839 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 0.47 (18839 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

CPED1 (HGNC:26159): (cadherin like and PC-esterase domain containing 1) Located in endoplasmic reticulum. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.2869-7702G>A		intron_variant		ENST00000310396.10
CPED1	XM_024446941.2	c.2356-7702G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.2869-7702G>A		intron_variant		1	NM_024913.5	P1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71371 AN: 151870 Hom.: 18809 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.470 AC: 71458 AN: 151988 Hom.: 18839 Cov.: 32 AF XY: 0.463 AC XY: 34369 AN XY: 74296

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.470

Alfa AF: 0.425 Hom.: 2343

Bravo AF: 0.484

Asia WGS AF: 0.502 AC: 1745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.1
Dann	Benign	0.75

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: rs2952556; hg19: chr7-120927792;