rs13245690

chr7-121145010-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CPED1	NM_024913.5	c.2055+2869A>G		intron_variant		ENST00000310396.10
LOC124901735	XR_007060494.1	n.35753T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.2055+2869A>G		intron_variant		1	NM_024913.5	P1
CPED1	ENST00000423795.5	c.1395+2869A>G		intron_variant		1
CPED1	ENST00000450913.6	c.2055+2869A>G		intron_variant		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

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.338

Alfa AF: 0.382 Hom.: 17708

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

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: rs13245690; hg19: chr7-120785064; COSMIC: COSV60008549; COSMIC: COSV60008549;