Genetic Variant CPED1:c.750-3delT (chr7-121099908-GT-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.750-3delT 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. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.19 ( 2969 hom., cov: 0)

Exomes 𝑓: 0.35 ( 1515 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 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.750-3delT		splice_region intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.750-3delT		splice_region 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.750-17delT	intron	N/A	ENSP00000309772.5	A4D0V7-1
CPED1	ENST00000450913.6	TSL:1	c.750-17delT	intron	N/A	ENSP00000406122.2	A4D0V7-2
CPED1	ENST00000423795.5	TSL:1	c.90-17delT	intron	N/A	ENSP00000415573.1	G5E9U2

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28104

AN:

148288

Hom.:

2971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0926

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.208

GnomAD2 exomes

AF:

0.318

AC:

52970

AN:

166798

AF XY:

0.325

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.424

Gnomad EAS exome

AF:

0.300

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.327

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.347

AC:

387034

AN:

1114450

Hom.:

1515

Cov.:

AF XY:

0.349

AC XY:

193737

AN XY:

555802

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.247

AC:

5613

AN:

22742

American (AMR)

AF:

0.291

AC:

8202

AN:

28218

Ashkenazi Jewish (ASJ)

AF:

0.413

AC:

8276

AN:

20034

East Asian (EAS)

AF:

0.325

AC:

8239

AN:

25366

South Asian (SAS)

AF:

0.351

AC:

24547

AN:

69998

European-Finnish (FIN)

AF:

0.279

AC:

10895

AN:

39028

Middle Eastern (MID)

AF:

0.351

AC:

1663

AN:

4734

European-Non Finnish (NFE)

AF:

0.353

AC:

303516

AN:

858768

Other (OTH)

AF:

0.353

AC:

16083

AN:

45562

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.394

Heterozygous variant carriers

13689

27378

41067

54756

68445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11570

23140

34710

46280

57850

<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:

0.189

AC:

28109

AN:

148368

Hom.:

2969

Cov.:

AF XY:

0.187

AC XY:

13521

AN XY:

72122

show subpopulations

African (AFR)

AF:

0.0927

AC:

3760

AN:

40550

American (AMR)

AF:

0.156

AC:

2324

AN:

14938

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1147

AN:

3432

East Asian (EAS)

AF:

0.109

AC:

551

AN:

5066

South Asian (SAS)

AF:

0.279

AC:

1305

AN:

4684

European-Finnish (FIN)

AF:

0.173

AC:

1655

AN:

9558

Middle Eastern (MID)

AF:

0.266

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.250

AC:

16696

AN:

66904

Other (OTH)

AF:

0.207

AC:

423

AN:

2044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

1032

2065

3097

4130

5162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.295

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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7-121099908-GTTTTTTT-GTTTTTT

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