Genetic Variant NM_024913.5:c.*300G>A (chr7-121295952-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.*300G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 241,020 control chromosomes in the GnomAD database, including 15,139 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 0.36 ( 9859 hom., cov: 32)

Exomes 𝑓: 0.33 ( 5280 hom. )

Consequence

CPED1
NM_024913.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.524

Publications

9 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=-0.66).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5 link	c.*300G>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000310396.10	NP_079189.4	A4D0V7-1
CPED1	XM_024446941.2 link	c.*300G>A		3_prime_UTR_variant	Exon 21 of 21		XP_024302709.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10 link	c.*300G>A		3_prime_UTR_variant	Exon 23 of 23	1	NM_024913.5	ENSP00000309772.5		A4D0V7-1

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54232

AN:

151934

Hom.:

9854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.402

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.366

GnomAD4 exome

AF:

0.333

AC:

29616

AN:

88968

Hom.:

5280

Cov.:

AF XY:

0.334

AC XY:

15099

AN XY:

45180

show subpopulations

African (AFR)

AF:

0.417

AC:

1223

AN:

2936

American (AMR)

AF:

0.269

AC:

1016

AN:

3774

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

1212

AN:

3132

East Asian (EAS)

AF:

0.267

AC:

1588

AN:

5952

South Asian (SAS)

AF:

0.379

AC:

2342

AN:

6182

European-Finnish (FIN)

AF:

0.293

AC:

1234

AN:

4218

Middle Eastern (MID)

AF:

0.368

AC:

176

AN:

478

European-Non Finnish (NFE)

AF:

0.333

AC:

18803

AN:

56522

Other (OTH)

AF:

0.350

AC:

2022

AN:

5774

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

944

1889

2833

3778

4722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

288

432

576

720

<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:

0.357

AC:

54256

AN:

152052

Hom.:

9859

Cov.:

AF XY:

0.352

AC XY:

26170

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.402

AC:

16661

AN:

41462

American (AMR)

AF:

0.303

AC:

4630

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.419

AC:

1456

AN:

3472

East Asian (EAS)

AF:

0.308

AC:

1594

AN:

5182

South Asian (SAS)

AF:

0.401

AC:

1932

AN:

4816

European-Finnish (FIN)

AF:

0.283

AC:

2985

AN:

10562

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.351

AC:

23878

AN:

67974

Other (OTH)

AF:

0.373

AC:

787

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1810

3620

5431

7241

9051

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.355

Hom.:

37671

Bravo

AF:

0.358

Asia WGS

AF:

0.387

AC:

1349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.9

(source)

DANN

Benign

0.78

PhyloP100

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over