dbSNP rs36113801: CPED1:c.541-1543delC (chr7-121062691-TC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024913.5(CPED1):c.541-1543delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,952 control chromosomes in the GnomAD database, including 35,266 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 35264 hom., cov: 0)

Exomes 𝑓: 1.0 ( 2 hom. )

Consequence

CPED1
NM_024913.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Publications

1 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5 link	c.541-1543delC		intron_variant	Intron 4 of 22	ENST00000310396.10	NP_079189.4	A4D0V7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10 link	c.541-1546delC		intron_variant	Intron 4 of 22	1	NM_024913.5	ENSP00000309772.5		A4D0V7-1

Frequencies

GnomAD3 genomes

AF:

0.666

AC:

101169

AN:

151830

Hom.:

35267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.890

Gnomad AMR

AF:

0.813

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.929

Gnomad SAS

AF:

0.715

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.736

Gnomad OTH

AF:

0.723

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.666

AC:

101186

AN:

151948

Hom.:

35264

Cov.:

AF XY:

0.664

AC XY:

49351

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.464

AC:

19208

AN:

41388

American (AMR)

AF:

0.813

AC:

12427

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.783

AC:

2717

AN:

3468

East Asian (EAS)

AF:

0.928

AC:

4797

AN:

5168

South Asian (SAS)

AF:

0.716

AC:

3443

AN:

4810

European-Finnish (FIN)

AF:

0.570

AC:

6009

AN:

10544

Middle Eastern (MID)

AF:

0.786

AC:

231

AN:

294

European-Non Finnish (NFE)

AF:

0.736

AC:

50031

AN:

67964

Other (OTH)

AF:

0.716

AC:

1513

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1561

3121

4682

6242

7803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.680

Hom.:

4433

Bravo

AF:

0.679

Asia WGS

AF:

0.730

AC:

2539

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.30

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over