Genetic Variant CPED1:c.750-4_750-3delTT (chr7-121099908-GTT-G) – 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.750-4_750-3delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.70 ( 36378 hom., cov: 0)

Exomes 𝑓: 0.47 ( 33747 hom. )

Failed GnomAD Quality Control

Consequence

CPED1
NM_024913.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Publications

3 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 = 0.82 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.750-4_750-3delTT		splice_region intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.750-4_750-3delTT		splice_region intron	N/A	NP_001099003.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CPED1	ENST00000310396.10	TSL:1 MANE Select	c.750-17_750-16delTT	intron	N/A	ENSP00000309772.5
CPED1	ENST00000450913.6	TSL:1	c.750-17_750-16delTT	intron	N/A	ENSP00000406122.2
CPED1	ENST00000423795.5	TSL:1	c.90-17_90-16delTT	intron	N/A	ENSP00000415573.1

Frequencies

GnomAD3 genomes

AF:

0.698

AC:

103823

AN:

148648

Hom.:

36346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.767

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.779

Gnomad ASJ

AF:

0.620

Gnomad EAS

AF:

0.842

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.671

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.698

GnomAD2 exomes

AF:

0.502

AC:

83747

AN:

166798

AF XY:

0.492

show subpopulations

Gnomad AFR exome

AF:

0.593

Gnomad AMR exome

AF:

0.528

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.590

Gnomad FIN exome

AF:

0.531

Gnomad NFE exome

AF:

0.498

Gnomad OTH exome

AF:

0.489

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.465

AC:

622606

AN:

1338460

Hom.:

33747

AF XY:

0.463

AC XY:

309215

AN XY:

667588

show subpopulations

African (AFR)

AF:

0.510

AC:

15158

AN:

29728

American (AMR)

AF:

0.522

AC:

19594

AN:

37570

Ashkenazi Jewish (ASJ)

AF:

0.455

AC:

10846

AN:

23852

East Asian (EAS)

AF:

0.532

AC:

19707

AN:

37020

South Asian (SAS)

AF:

0.409

AC:

32305

AN:

78906

European-Finnish (FIN)

AF:

0.487

AC:

22728

AN:

46704

Middle Eastern (MID)

AF:

0.541

AC:

2902

AN:

5366

European-Non Finnish (NFE)

AF:

0.462

AC:

473380

AN:

1023928

Other (OTH)

AF:

0.469

AC:

25986

AN:

55386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

14350

28699

43049

57398

71748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17418

34836

52254

69672

87090

<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:

0.699

AC:

103899

AN:

148734

Hom.:

36378

Cov.:

AF XY:

0.700

AC XY:

50609

AN XY:

72334

show subpopulations

African (AFR)

AF:

0.767

AC:

31121

AN:

40578

American (AMR)

AF:

0.779

AC:

11678

AN:

14992

Ashkenazi Jewish (ASJ)

AF:

0.620

AC:

2130

AN:

3438

East Asian (EAS)

AF:

0.842

AC:

4270

AN:

5074

South Asian (SAS)

AF:

0.544

AC:

2541

AN:

4674

European-Finnish (FIN)

AF:

0.671

AC:

6513

AN:

9700

Middle Eastern (MID)

AF:

0.727

AC:

205

AN:

282

European-Non Finnish (NFE)

AF:

0.646

AC:

43310

AN:

67036

Other (OTH)

AF:

0.701

AC:

1438

AN:

2050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1512

3023

4535

6046

7558

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:

0.489

Hom.:

136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.3

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