rs798948

chr7-121124519-C-Achr7-121124519-C-G

Variant summary

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

The NM_024913.5(CPED1):c.1061+46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 1,322,402 control chromosomes in the GnomAD database, including 533,691 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 0.90 (61196 hom., cov: 31)
  • Exomes 𝑓: 0.90 (472495 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.1061+46C>A		intron_variant		ENST00000310396.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.1061+46C>A		intron_variant		1	NM_024913.5	P1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136287 AN: 151996 Hom.: 61151 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.911

GnomAD3 exomes AF: 0.887 AC: 81553 AN: 91958 Hom.: 36212 AF XY: 0.887 AC XY: 45308 AN XY: 51096

Gnomad AFR exome AF: 0.872

Gnomad AMR exome AF: 0.910

Gnomad ASJ exome AF: 0.962

Gnomad EAS exome AF: 0.940

Gnomad SAS exome AF: 0.841

Gnomad FIN exome AF: 0.855

Gnomad NFE exome AF: 0.894

Gnomad OTH exome AF: 0.887

GnomAD4 exome AF: 0.898 AC: 1051020 AN: 1170288 Hom.: 472495 Cov.: 17 AF XY: 0.897 AC XY: 514044 AN XY: 572996

Gnomad4 AFR exome AF: 0.879

Gnomad4 AMR exome AF: 0.926

Gnomad4 ASJ exome AF: 0.960

Gnomad4 EAS exome AF: 0.963

Gnomad4 SAS exome AF: 0.844

Gnomad4 FIN exome AF: 0.856

Gnomad4 NFE exome AF: 0.899

Gnomad4 OTH exome AF: 0.910

GnomAD4 genome AF: 0.897 AC: 136391 AN: 152114 Hom.: 61196 Cov.: 31 AF XY: 0.896 AC XY: 66613 AN XY: 74366

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.912

Alfa AF: 0.891 Hom.: 7519

Bravo AF: 0.905

Asia WGS AF: 0.890 AC: 3085 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.50

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: rs798948; hg19: chr7-120764573;