rs2110277

Positions:

• chr7-121062756-A-G
• chr7-121062756-A-T

Variant summary

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

The NM_024913.5(CPED1):​c.541-1482A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,034 control chromosomes in the GnomAD database, including 47,571 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 0.79 (47568 hom., cov: 31)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.541-1482A>G		intron_variant		ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.541-1482A>G		intron_variant		1	NM_024913.5	ENSP00000309772	P1

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119816 AN: 151908 Hom.: 47524 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 6 AN XY: 6

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.789 AC: 119909 AN: 152028 Hom.: 47568 Cov.: 31 AF XY: 0.786 AC XY: 58370 AN XY: 74266

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.810

Alfa AF: 0.768 Hom.: 5625

Bravo AF: 0.810

Asia WGS AF: 0.757 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.55

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: rs2110277; hg19: chr7-120702810;