7-121042218-C-A

Variant names:

• chr7-121042218-C-A
• rs12537243
• NM_024913.5:c.434-4669C>A

Variant summary

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

The NM_024913.5(CPED1):​c.434-4669C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 151,726 control chromosomes in the GnomAD database, including 511 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 0.070 (511 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 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.434-4669C>A		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.434-4669C>A		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.434-4669C>A		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.434-4669C>A		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000495036.5	TSL:1	n.881-4669C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10641 AN: 151654 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0701 AC: 10638 AN: 151726 Hom.: 511 Cov.: 32 AF XY: 0.0676 AC XY: 5012 AN XY: 74100

African (AFR) AF: 0.0203 AC: 838 AN: 41346

American (AMR) AF: 0.0564 AC: 861 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0117 AC: 56 AN: 4806

European-Finnish (FIN) AF: 0.0923 AC: 963 AN: 10436

Middle Eastern (MID) AF: 0.0483 AC: 14 AN: 290

European-Non Finnish (NFE) AF: 0.111 AC: 7525 AN: 67936

Other (OTH) AF: 0.0723 AC: 152 AN: 2102

Alfa AF: 0.0490 Hom.: 54

Bravo AF: 0.0646

Asia WGS AF: 0.00751 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.099
DANN	Benign	0.32
PhyloP100		-1.3
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: rs12537243; hg19: chr7-120682272;