rs12537243

chr7-121042218-C-Achr7-121042218-C-T

Variant summary

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

The NM_024913.5(CPED1):c.434-4669C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 151,726 control chromosomes in the GnomAD database, including 511 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 0.070 (511 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.434-4669C>A		intron_variant		ENST00000310396.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.434-4669C>A		intron_variant		1	NM_024913.5	P1

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10641 AN: 151654 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0701 AC: 10638 AN: 151726 Hom.: 511 Cov.: 32 AF XY: 0.0676 AC XY: 5012 AN XY: 74100

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0117

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0490 Hom.: 54

Bravo AF: 0.0646

Asia WGS AF: 0.00751 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.099
Dann	Benign	0.32

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: rs12537243; hg19: chr7-120682272;