Genetic Variant CPED1:p.Asp774Asn (chr7-121261641-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000450913.6(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. 12/16 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
ENST00000450913.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Publications

30 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CPED1	NM_024913.5 link	c.2311-4586G>A		intron_variant	Intron 18 of 22	ENST00000310396.10	NP_079189.4	A4D0V7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CPED1	ENST00000450913.6 link	c.2320G>A	p.Asp774Asn	missense_variant	Exon 18 of 18	1		ENSP00000406122.2	A4D0V7-2
CPED1	ENST00000423795.5 link	c.1660G>A	p.Asp554Asn	missense_variant	Exon 16 of 16	1		ENSP00000415573.1	G5E9U2
CPED1	ENST00000310396.10 link	c.2311-4586G>A		intron_variant	Intron 18 of 22	1	NM_024913.5	ENSP00000309772.5	A4D0V7-1
CPED1	ENST00000466055.1 link	n.353G>A		non_coding_transcript_exon_variant	Exon 4 of 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

GnomAD2 exomes

AF:

0.350

AC:

84599

AN:

241372

AF XY:

0.355

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 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

African (AFR)

AF:

0.501

AC:

16713

AN:

33346

American (AMR)

AF:

0.238

AC:

10507

AN:

44196

Ashkenazi Jewish (ASJ)

AF:

0.448

AC:

11653

AN:

26014

East Asian (EAS)

AF:

0.117

AC:

4621

AN:

39492

South Asian (SAS)

AF:

0.373

AC:

31930

AN:

85576

European-Finnish (FIN)

AF:

0.366

AC:

19465

AN:

53134

Middle Eastern (MID)

AF:

0.424

AC:

2439

AN:

5748

European-Non Finnish (NFE)

AF:

0.383

AC:

425223

AN:

1109766

Other (OTH)

AF:

0.382

AC:

22952

AN:

60148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

18097

36194

54290

72387

90484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13246

26492

39738

52984

66230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.396

AC:

60138

AN:

151680

Hom.:

12553

Cov.:

AF XY:

0.391

AC XY:

29006

AN XY:

74096

show subpopulations

African (AFR)

AF:

0.500

AC:

20663

AN:

41350

American (AMR)

AF:

0.303

AC:

4613

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.460

AC:

1591

AN:

3462

East Asian (EAS)

AF:

0.127

AC:

651

AN:

5122

South Asian (SAS)

AF:

0.356

AC:

1714

AN:

4814

European-Finnish (FIN)

AF:

0.363

AC:

3830

AN:

10538

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25835

AN:

67856

Other (OTH)

AF:

0.404

AC:

851

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.389

Hom.:

18883

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

(source)

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

PhyloP100

-0.45

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

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over