rs59228206

chr7-121128565-T-TC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_024913.5(CPED1):c.1407+80dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 751,382 control chromosomes in the GnomAD database, including 1,433 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.069 (484 hom., cov: 31)
  • Exomes 𝑓: 0.050 (949 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.1407+80dup		intron_variant		ENST00000310396.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.1407+80dup		intron_variant		1	NM_024913.5	P1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10490 AN: 152074 Hom.: 481 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0708

GnomAD4 exome AF: 0.0504 AC: 30225 AN: 599190 Hom.: 949 AF XY: 0.0492 AC XY: 15901 AN XY: 323216

Gnomad4 AFR exome AF: 0.115

Gnomad4 AMR exome AF: 0.0346

Gnomad4 ASJ exome AF: 0.0463

Gnomad4 EAS exome AF: 0.0000564

Gnomad4 SAS exome AF: 0.0200

Gnomad4 FIN exome AF: 0.0493

Gnomad4 NFE exome AF: 0.0595

Gnomad4 OTH exome AF: 0.0510

GnomAD4 genome AF: 0.0691 AC: 10514 AN: 152192 Hom.: 484 Cov.: 31 AF XY: 0.0659 AC XY: 4905 AN XY: 74404

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0461

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0663 Hom.: 46

Bravo AF: 0.0728

Asia WGS AF: 0.0160 AC: 56 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs59228206; hg19: chr7-120768619;