rs55666906

Positions:

• chr7-120989162-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.-231-229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0728 in 167,578 control chromosomes in the GnomAD database, including 641 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 0.072 (582 hom., cov: 32)
  • Exomes 𝑓: 0.080 (59 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.-231-229G>A		intron_variant		ENST00000310396.10
CPED1	XM_047420856.1	c.-231-229G>A		intron_variant
CPED1	XM_047420857.1	c.-231-229G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.-231-229G>A		intron_variant		1	NM_024913.5	P1
CPED1	ENST00000428526.5	c.-460G>A		5_prime_UTR_variant	1/12	2
CPED1	ENST00000340646.9	c.-231-229G>A		intron_variant		5
CPED1	ENST00000495036.5			upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10955 AN: 152106 Hom.: 578 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0645

GnomAD4 exome AF: 0.0800 AC: 1229 AN: 15354 Hom.: 59 Cov.: 0 AF XY: 0.0769 AC XY: 601 AN XY: 7818

Gnomad4 AFR exome AF: 0.00926

Gnomad4 AMR exome AF: 0.0535

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0598

Gnomad4 FIN exome AF: 0.0939

Gnomad4 NFE exome AF: 0.0904

Gnomad4 OTH exome AF: 0.0875

GnomAD4 genome AF: 0.0720 AC: 10964 AN: 152224 Hom.: 582 Cov.: 32 AF XY: 0.0729 AC XY: 5425 AN XY: 74412

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0549

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0909 Hom.: 153

Bravo AF: 0.0643

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	16
DANN	Benign	0.85

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: rs55666906; hg19: chr7-120629216;