Genetic Variant CPED1:c.1061+46C>A (chr7-121124519-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024913.5(CPED1):c.1061+46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 1,322,402 control chromosomes in the GnomAD database, including 533,691 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 0.90 ( 61196 hom., cov: 31)

Exomes 𝑓: 0.90 ( 472495 hom. )

Consequence

CPED1
NM_024913.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0700

Publications

7 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:

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 (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.1061+46C>A		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.1061+46C>A		intron	N/A	NP_001099003.1	Q9H6Q5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CPED1	ENST00000310396.10	TSL:1 MANE Select	c.1061+46C>A	intron	N/A	ENSP00000309772.5	A4D0V7-1
CPED1	ENST00000450913.6	TSL:1	c.1061+46C>A	intron	N/A	ENSP00000406122.2	A4D0V7-2
CPED1	ENST00000423795.5	TSL:1	c.401+46C>A	intron	N/A	ENSP00000415573.1	G5E9U2

Frequencies

GnomAD3 genomes

AF:

0.897

AC:

136287

AN:

151996

Hom.:

61151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.878

Gnomad AMI

AF:

0.952

Gnomad AMR

AF:

0.937

Gnomad ASJ

AF:

0.958

Gnomad EAS

AF:

0.957

Gnomad SAS

AF:

0.833

Gnomad FIN

AF:

0.860

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

0.900

Gnomad OTH

AF:

0.911

GnomAD2 exomes

AF:

0.887

AC:

81553

AN:

91958

AF XY:

0.887

show subpopulations

Gnomad AFR exome

AF:

0.872

Gnomad AMR exome

AF:

0.910

Gnomad ASJ exome

AF:

0.962

Gnomad EAS exome

AF:

0.940

Gnomad FIN exome

AF:

0.855

Gnomad NFE exome

AF:

0.894

Gnomad OTH exome

AF:

0.887

GnomAD4 exome

AF:

0.898

AC:

1051020

AN:

1170288

Hom.:

472495

Cov.:

AF XY:

0.897

AC XY:

514044

AN XY:

572996

show subpopulations

African (AFR)

AF:

0.879

AC:

21828

AN:

24820

American (AMR)

AF:

0.926

AC:

15620

AN:

16860

Ashkenazi Jewish (ASJ)

AF:

0.960

AC:

17999

AN:

18742

East Asian (EAS)

AF:

0.963

AC:

28695

AN:

29790

South Asian (SAS)

AF:

0.844

AC:

42887

AN:

50806

European-Finnish (FIN)

AF:

0.856

AC:

34551

AN:

40366

Middle Eastern (MID)

AF:

0.958

AC:

3978

AN:

4152

European-Non Finnish (NFE)

AF:

0.899

AC:

842206

AN:

937216

Other (OTH)

AF:

0.910

AC:

43256

AN:

47536

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

4388

8776

13164

17552

21940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19206

38412

57618

76824

96030

<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:

0.897

AC:

136391

AN:

152114

Hom.:

61196

Cov.:

AF XY:

0.896

AC XY:

66613

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.878

AC:

36440

AN:

41514

American (AMR)

AF:

0.937

AC:

14324

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.958

AC:

3324

AN:

3468

East Asian (EAS)

AF:

0.957

AC:

4956

AN:

5180

South Asian (SAS)

AF:

0.833

AC:

4015

AN:

4818

European-Finnish (FIN)

AF:

0.860

AC:

9063

AN:

10542

Middle Eastern (MID)

AF:

0.993

AC:

292

AN:

294

European-Non Finnish (NFE)

AF:

0.900

AC:

61187

AN:

67998

Other (OTH)

AF:

0.912

AC:

1924

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

722

1444

2167

2889

3611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.890

Hom.:

7820

Bravo

AF:

0.905

Asia WGS

AF:

0.890

AC:

3085

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.2

(source)

DANN

Benign

0.50

PhyloP100

0.070

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over