Variant rs10953934 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001105533.1(CPED1):c.2320G>A(p.Asp774Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,609,100 control chromosomes in the GnomAD database, including 116,955 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 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: 𝑓 0.40 ( 12553 hom., cov: 31)

Exomes 𝑓: 0.37 ( 104402 hom. )

Consequence

CPED1
NM_001105533.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

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]

CPED1 links:

LOC124901735 (HGNC:):

LOC124901735 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.02728285E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5 link	c.2311-4586G>A		intron_variant		ENST00000310396.10	NP_079189.4	A4D0V7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CPED1	ENST00000450913.6 link	c.2320G>A	p.Asp774Asn	missense_variant	18/18	1		ENSP00000406122.2	A4D0V7-2
CPED1	ENST00000423795.5 link	c.1660G>A	p.Asp554Asn	missense_variant	16/16	1		ENSP00000415573.1	G5E9U2
CPED1	ENST00000310396.10 link	c.2311-4586G>A		intron_variant		1	NM_024913.5	ENSP00000309772.5	A4D0V7-1
CPED1	ENST00000466055.1 link	n.353G>A		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60042

AN:

151560

Hom.:

12519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.363

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.396

GnomAD3 exomes

AF:

0.350

AC:

84599

AN:

241372

Hom.:

15878

AF XY:

0.355

AC XY:

46563

AN XY:

131024

show subpopulations

Gnomad AFR exome

AF:

0.508

Gnomad AMR exome

AF:

0.232

Gnomad ASJ exome

AF:

0.449

Gnomad EAS exome

AF:

0.132

Gnomad SAS exome

AF:

0.375

Gnomad FIN exome

AF:

0.371

Gnomad NFE exome

AF:

0.381

Gnomad OTH exome

AF:

0.366

GnomAD4 exome

AF:

0.374

AC:

545503

AN:

1457420

Hom.:

104402

Cov.:

AF XY:

0.375

AC XY:

271466

AN XY:

724656

show subpopulations

Gnomad4 AFR exome

AF:

0.501

Gnomad4 AMR exome

AF:

0.238

Gnomad4 ASJ exome

AF:

0.448

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.373

Gnomad4 FIN exome

AF:

0.366

Gnomad4 NFE exome

AF:

0.383

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

AF:

0.396

AC:

60138

AN:

151680

Hom.:

12553

Cov.:

AF XY:

0.391

AC XY:

29006

AN XY:

74096

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.460

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.363

Gnomad4 NFE

AF:

0.381

Gnomad4 OTH

AF:

0.404

Alfa

AF:

0.391

Hom.:

14850

Bravo

AF:

0.396

TwinsUK

AF:

0.369

AC:

1370

ALSPAC

AF:

0.382

AC:

1474

ESP6500AA

AF:

0.493

AC:

1858

ESP6500EA

AF:

0.389

AC:

3188

ExAC

AF:

0.353

AC:

42612

Asia WGS

AF:

0.309

AC:

1075

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.2

DANN

Benign

0.30

DEOGEN2

Benign

0.0051

.;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00012

LIST_S2

Benign

0.25

T;T

MetaRNN

Benign

0.00010

T;T

MetaSVM

Benign

-0.95

PROVEAN

Benign

-0.040

N;N

REVEL

Benign

0.021

Sift

Pathogenic

0.0

D;D

Polyphen

0.0

B;B

Vest4

0.16

ClinPred

0.013

GERP RS

1.9

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over