NM_024913.5:c.919-5486G>A

Variant names:

• chr7-121118845-G-A
• rs798943
• NM_024913.5:c.919-5486G>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.919-5486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,722 control chromosomes in the GnomAD database, including 9,308 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 0.34 (9308 hom., cov: 30)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 17 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.919-5486G>A		intron_variant	Intron 7 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.919-5486G>A		intron_variant	Intron 7 of 22	1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52191 AN: 151604 Hom.: 9302 Cov.: 30

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.344 AC: 52223 AN: 151722 Hom.: 9308 Cov.: 30 AF XY: 0.340 AC XY: 25170 AN XY: 74136

African (AFR) AF: 0.325 AC: 13419 AN: 41332

American (AMR) AF: 0.270 AC: 4114 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3468

East Asian (EAS) AF: 0.112 AC: 576 AN: 5146

South Asian (SAS) AF: 0.369 AC: 1770 AN: 4796

European-Finnish (FIN) AF: 0.293 AC: 3090 AN: 10536

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26209 AN: 67906

Other (OTH) AF: 0.357 AC: 751 AN: 2106

Alfa AF: 0.369 Hom.: 15521

Bravo AF: 0.341

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.62
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: rs798943; hg19: chr7-120758899; COSMIC: COSV60013798;