chr7-121015831-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024913.5(CPED1):​c.416C>A​(p.Pro139Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000711 in 1,405,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P139L) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.1e-7 ( 0 hom. )

Consequence

CPED1
NM_024913.5 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.042500883).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CPED1NM_024913.5 linkc.416C>A p.Pro139Gln missense_variant Exon 3 of 23 ENST00000310396.10 NP_079189.4 A4D0V7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CPED1ENST00000310396.10 linkc.416C>A p.Pro139Gln missense_variant Exon 3 of 23 1 NM_024913.5 ENSP00000309772.5 A4D0V7-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.11e-7
AC:
1
AN:
1405688
Hom.:
0
Cov.:
31
AF XY:
0.00000143
AC XY:
1
AN XY:
696964
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.17e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
0.45
DANN
Benign
0.83
DEOGEN2
Benign
0.0013
T;T;.;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.018
N
LIST_S2
Benign
0.35
T;T;T;T
M_CAP
Benign
0.0077
T
MetaRNN
Benign
0.043
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N;.;.;N
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.090
N;N;N;N
REVEL
Benign
0.034
Sift
Benign
0.51
T;T;T;T
Sift4G
Benign
0.51
T;T;T;T
Polyphen
0.0020
B;.;.;B
Vest4
0.21
MutPred
0.34
Loss of loop (P = 0.0603);Loss of loop (P = 0.0603);Loss of loop (P = 0.0603);Loss of loop (P = 0.0603);
MVP
0.030
MPC
0.057
ClinPred
0.028
T
GERP RS
0.42
Varity_R
0.021
gMVP
0.15

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.19
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-120655885; API