rs13245690

Variant names:

• chr7-121145010-A-G
• rs13245690
• NM_024913.5:c.2055+2869A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024913.5(CPED1):​c.2055+2869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,770 control chromosomes in the GnomAD database, including 8,306 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 0.32 (8306 hom., cov: 31)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• Publications: 38 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]

LOC124901735 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.2055+2869A>G		intron_variant	Intron 16 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.2055+2869A>G		intron_variant	Intron 16 of 22	1	NM_024913.5	ENSP00000309772.5
CPED1	ENST00000450913.6	c.2055+2869A>G		intron_variant	Intron 15 of 17	1		ENSP00000406122.2
CPED1	ENST00000423795.5	c.1395+2869A>G		intron_variant	Intron 13 of 15	1		ENSP00000415573.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48687 AN: 151652 Hom.: 8302 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.321 AC: 48710 AN: 151770 Hom.: 8306 Cov.: 31 AF XY: 0.318 AC XY: 23568 AN XY: 74200

African (AFR) AF: 0.249 AC: 10319 AN: 41466

American (AMR) AF: 0.258 AC: 3923 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3468

East Asian (EAS) AF: 0.113 AC: 582 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3086 AN: 10558

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26038 AN: 67768

Other (OTH) AF: 0.338 AC: 711 AN: 2106

Alfa AF: 0.371 Hom.: 38881

Bravo AF: 0.314

Asia WGS AF: 0.270 AC: 938 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.69
PhyloP100		0.91
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: rs13245690; hg19: chr7-120785064; COSMIC: COSV60008549; COSMIC: COSV60008549;