7-121020676-A-G

Variant names:

• chr7-121020676-A-G
• rs2215786
• NM_024913.5:c.433+4828A>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.433+4828A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 151,670 control chromosomes in the GnomAD database, including 47,930 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 (47930 hom., cov: 31)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 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.433+4828A>G		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.433+4828A>G		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.433+4828A>G		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.433+4828A>G		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000495036.5	TSL:1	n.880+4828A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120132 AN: 151552 Hom.: 47878 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.793 AC: 120235 AN: 151670 Hom.: 47930 Cov.: 31 AF XY: 0.794 AC XY: 58899 AN XY: 74144

African (AFR) AF: 0.750 AC: 31072 AN: 41416

American (AMR) AF: 0.865 AC: 13152 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2828 AN: 3464

East Asian (EAS) AF: 0.938 AC: 4860 AN: 5180

South Asian (SAS) AF: 0.898 AC: 4330 AN: 4822

European-Finnish (FIN) AF: 0.701 AC: 7381 AN: 10536

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 53917 AN: 67742

Other (OTH) AF: 0.807 AC: 1696 AN: 2102

Alfa AF: 0.793 Hom.: 7244

Bravo AF: 0.802

Asia WGS AF: 0.858 AC: 2983 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.49
PhyloP100		-0.77
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: rs2215786; hg19: chr7-120660730;