NM_024913.5:c.540+8380T>G

Variant names:

• chr7-121055373-T-G
• rs12706309
• NM_024913.5:c.540+8380T>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.540+8380T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,814 control chromosomes in the GnomAD database, including 35,527 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 0.66 (35527 hom., cov: 33)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.793 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.540+8380T>G		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.540+8380T>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.540+8380T>G		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.540+8380T>G		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000942586.1		c.540+8380T>G		intron	N/A	ENSP00000612645.1

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99766 AN: 151696 Hom.: 35532 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.657 AC: 99768 AN: 151814 Hom.: 35527 Cov.: 33 AF XY: 0.660 AC XY: 49018 AN XY: 74230

African (AFR) AF: 0.360 AC: 14930 AN: 41454

American (AMR) AF: 0.805 AC: 12301 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2636 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4015 AN: 5182

South Asian (SAS) AF: 0.761 AC: 3675 AN: 4830

European-Finnish (FIN) AF: 0.689 AC: 7164 AN: 10396

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52613 AN: 67886

Other (OTH) AF: 0.685 AC: 1448 AN: 2114

Alfa AF: 0.694 Hom.: 4805

Bravo AF: 0.652

Asia WGS AF: 0.665 AC: 2287 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.2
DANN	Benign	0.53
PhyloP100		-0.58
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: rs12706309; hg19: chr7-120695427;