NM_024913.5:c.1652C>A

Variant names:

• chr7-121136043-C-A
• rs41281692
• NM_024913.5:c.1652C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024913.5(CPED1):​c.1652C>A​(p.Ala551Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CPED1 NM_024913.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 30 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06931308).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.1652C>A	p.Ala551Glu	missense_variant	Exon 14 of 23	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.1652C>A	p.Ala551Glu	missense_variant	Exon 14 of 23	1	NM_024913.5	ENSP00000309772.5
CPED1	ENST00000450913.6	c.1652C>A	p.Ala551Glu	missense_variant	Exon 13 of 18	1		ENSP00000406122.2
CPED1	ENST00000423795.5	c.992C>A	p.Ala331Glu	missense_variant	Exon 11 of 16	1		ENSP00000415573.1
CPED1	ENST00000443817.1	c.992C>A	p.Ala331Glu	missense_variant	Exon 10 of 10	1		ENSP00000391952.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1343736 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 667146

African (AFR) AF: 0.00 AC: 0 AN: 28818

American (AMR) AF: 0.00 AC: 0 AN: 26164

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23206

East Asian (EAS) AF: 0.00 AC: 0 AN: 33922

South Asian (SAS) AF: 0.00 AC: 0 AN: 67610

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5282

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1053032

Other (OTH) AF: 0.00 AC: 0 AN: 55080

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 11784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	0.099
DANN	Benign	0.58
DEOGEN2	Benign	0.0019	T;.;T;.
Eigen	Benign	-0.90
Eigen_PC	Benign	-0.96
FATHMM_MKL	Benign	0.064	N
LIST_S2	Benign	0.35	T;T;T;T
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.069	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	M;M;.;.
PhyloP100		-0.58
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.75	N;N;N;N
REVEL	Benign	0.011
Sift	Benign	0.27	T;T;T;D
Sift4G	Uncertain	0.058	T;T;T;T
Polyphen		0.047	B;B;B;.
Vest4		0.11
MutPred		0.33		Gain of solvent accessibility (P = 0.005);Gain of solvent accessibility (P = 0.005);.;.;
MVP		0.055
MPC		0.061
ClinPred		0.11	T
GERP RS		-0.51
Varity_R		0.11
gMVP		0.32
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs41281692; hg19: chr7-120776097;