7-121048409-C-T

Variant names:

• chr7-121048409-C-T
• rs2160010
• NM_024913.5:c.540+1416C>T

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+1416C>T 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 152,140 control chromosomes in the GnomAD database, including 35,617 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 (35617 hom., cov: 33)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 3 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=-0.89).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.540+1416C>T		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.540+1416C>T		intron	N/A	NP_001099003.1	Q9H6Q5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	ENST00000310396.10	TSL:1 MANE Select	c.540+1416C>T		intron	N/A	ENSP00000309772.5	A4D0V7-1
	CPED1	ENST00000450913.6	TSL:1	c.540+1416C>T		intron	N/A	ENSP00000406122.2	A4D0V7-2
	CPED1	ENST00000495036.5	TSL:1	n.987+1416C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100018 AN: 152022 Hom.: 35622 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.657 AC: 100020 AN: 152140 Hom.: 35617 Cov.: 33 AF XY: 0.661 AC XY: 49133 AN XY: 74364

African (AFR) AF: 0.360 AC: 14940 AN: 41468

American (AMR) AF: 0.805 AC: 12320 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2636 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4007 AN: 5166

South Asian (SAS) AF: 0.760 AC: 3670 AN: 4826

European-Finnish (FIN) AF: 0.690 AC: 7302 AN: 10582

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52709 AN: 68004

Other (OTH) AF: 0.686 AC: 1449 AN: 2112

Alfa AF: 0.746 Hom.: 23846

Bravo AF: 0.652

Asia WGS AF: 0.665 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		0.29
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: rs2160010; hg19: chr7-120688463;