Genetic Variant CPED1:c.-231-229G>A (chr7-120989162-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 NM_024913.5(CPED1):c.-231-229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0728 in 167,578 control chromosomes in the GnomAD database, including 641 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 0.072 ( 582 hom., cov: 32)

Exomes 𝑓: 0.080 ( 59 hom. )

Consequence

CPED1
NM_024913.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.68

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0991 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.-231-229G>A		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.-460G>A		upstream_gene	N/A	NP_001099003.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CPED1	ENST00000310396.10	TSL:1 MANE Select	c.-231-229G>A	intron	N/A	ENSP00000309772.5
CPED1	ENST00000428526.5	TSL:2	c.-460G>A	5_prime_UTR	Exon 1 of 12	ENSP00000398082.1
CPED1	ENST00000340646.9	TSL:5	c.-231-229G>A	intron	N/A	ENSP00000345235.5

Frequencies

GnomAD3 genomes

AF:

0.0720

AC:

10955

AN:

152106

Hom.:

578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0191

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.0464

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.0553

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0645

GnomAD4 exome

AF:

0.0800

AC:

1229

AN:

15354

Hom.:

Cov.:

AF XY:

0.0769

AC XY:

601

AN XY:

7818

show subpopulations

African (AFR)

AF:

0.00926

AC:

AN:

108

American (AMR)

AF:

0.0535

AC:

AN:

1776

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

AN:

218

East Asian (EAS)

AF:

0.00

AC:

AN:

358

South Asian (SAS)

AF:

0.0598

AC:

106

AN:

1772

European-Finnish (FIN)

AF:

0.0939

AC:

AN:

490

Middle Eastern (MID)

AF:

0.100

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0904

AC:

881

AN:

9746

Other (OTH)

AF:

0.0875

AC:

AN:

846

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

119

178

238

297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0720

AC:

10964

AN:

152224

Hom.:

582

Cov.:

AF XY:

0.0729

AC XY:

5425

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0190

AC:

789

AN:

41546

American (AMR)

AF:

0.0463

AC:

708

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

451

AN:

3472

East Asian (EAS)

AF:

0.00367

AC:

AN:

5178

South Asian (SAS)

AF:

0.0549

AC:

265

AN:

4828

European-Finnish (FIN)

AF:

0.147

AC:

1553

AN:

10582

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6873

AN:

67998

Other (OTH)

AF:

0.0723

AC:

153

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

521

1041

1562

2082

2603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0909

Hom.:

153

Bravo

AF:

0.0643

Asia WGS

AF:

0.0750

AC:

261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

1.7

PromoterAI

-0.048

Neutral

(source)

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