NM_024913.5:c.616+10333C>T

Variant names:

• chr7-121074646-C-T
• rs10251692
• NM_024913.5:c.616+10333C>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.616+10333C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 150,646 control chromosomes in the GnomAD database, including 16,390 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 0.46 (16390 hom., cov: 28)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.616+10333C>T		intron_variant	Intron 5 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.616+10333C>T		intron_variant	Intron 5 of 22	1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 69800 AN: 150524 Hom.: 16386 Cov.: 28

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.536

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.464 AC: 69843 AN: 150646 Hom.: 16390 Cov.: 28 AF XY: 0.471 AC XY: 34624 AN XY: 73554

African (AFR) AF: 0.443 AC: 18207 AN: 41104

American (AMR) AF: 0.595 AC: 8957 AN: 15058

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3466

East Asian (EAS) AF: 0.617 AC: 3125 AN: 5062

South Asian (SAS) AF: 0.378 AC: 1790 AN: 4730

European-Finnish (FIN) AF: 0.479 AC: 4917 AN: 10264

Middle Eastern (MID) AF: 0.528 AC: 151 AN: 286

European-Non Finnish (NFE) AF: 0.436 AC: 29528 AN: 67688

Other (OTH) AF: 0.487 AC: 1014 AN: 2084

Alfa AF: 0.449 Hom.: 58387

Bravo AF: 0.472

Asia WGS AF: 0.464 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		0.21
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: rs10251692; hg19: chr7-120714700;