rs59228206

Variant names:

• chr7-121128565-T-TC
• rs59228206
• NM_024913.5:c.1407+80dupC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024913.5(CPED1):​c.1407+80dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 751,382 control chromosomes in the GnomAD database, including 1,433 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.069 (484 hom., cov: 31)
  • Exomes 𝑓: 0.050 (949 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.1407+80dupC		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.1407+80dupC		intron	N/A	NP_001099003.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	ENST00000310396.10	TSL:1 MANE Select	c.1407+79_1407+80insC		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.1407+79_1407+80insC		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000423795.5	TSL:1	c.747+79_747+80insC		intron	N/A	ENSP00000415573.1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10490 AN: 152074 Hom.: 481 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0708

GnomAD4 exome AF: 0.0504 AC: 30225 AN: 599190 Hom.: 949 AF XY: 0.0492 AC XY: 15901 AN XY: 323216

African (AFR) AF: 0.115 AC: 1848 AN: 16020

American (AMR) AF: 0.0346 AC: 1165 AN: 33622

Ashkenazi Jewish (ASJ) AF: 0.0463 AC: 832 AN: 17982

East Asian (EAS) AF: 0.0000564 AC: 2 AN: 35442

South Asian (SAS) AF: 0.0200 AC: 1161 AN: 57944

European-Finnish (FIN) AF: 0.0493 AC: 2463 AN: 49982

Middle Eastern (MID) AF: 0.0319 AC: 109 AN: 3416

European-Non Finnish (NFE) AF: 0.0595 AC: 21048 AN: 353458

Other (OTH) AF: 0.0510 AC: 1597 AN: 31324

GnomAD4 genome AF: 0.0691 AC: 10514 AN: 152192 Hom.: 484 Cov.: 31 AF XY: 0.0659 AC XY: 4905 AN XY: 74404

African (AFR) AF: 0.113 AC: 4695 AN: 41526

American (AMR) AF: 0.0502 AC: 767 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5196

South Asian (SAS) AF: 0.0155 AC: 75 AN: 4828

European-Finnish (FIN) AF: 0.0461 AC: 488 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4145 AN: 67994

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0663 Hom.: 46

Bravo AF: 0.0728

Asia WGS AF: 0.0160 AC: 56 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs59228206; hg19: chr7-120768619;