rs10241888

chr7-121295952-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.*300G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 241,020 control chromosomes in the GnomAD database, including 15,139 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 0.36 (9859 hom., cov: 32)
  • Exomes 𝑓: 0.33 (5280 hom.)
• Consequence: CPED1 NM_024913.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524

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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.*300G>A		3_prime_UTR_variant	23/23	ENST00000310396.10
CPED1	XM_024446941.2	c.*300G>A		3_prime_UTR_variant	21/21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.*300G>A		3_prime_UTR_variant	23/23	1	NM_024913.5	P1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54232 AN: 151934 Hom.: 9854 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.333 AC: 29616 AN: 88968 Hom.: 5280 Cov.: 0 AF XY: 0.334 AC XY: 15099 AN XY: 45180

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.269

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.379

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.357 AC: 54256 AN: 152052 Hom.: 9859 Cov.: 32 AF XY: 0.352 AC XY: 26170 AN XY: 74324

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.373

Alfa AF: 0.356 Hom.: 16461

Bravo AF: 0.358

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	8.9
Dann	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10241888; hg19: chr7-120936006; COSMIC: COSV60001723;