Genetic Variant GPCPD1:c.1395+19A>G (chr20-5561446-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019593.5(GPCPD1):c.1395+19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,388,054 control chromosomes in the GnomAD database, including 33,176 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 0.25 ( 5069 hom., cov: 33)

Exomes 𝑓: 0.21 ( 28107 hom. )

Consequence

GPCPD1
NM_019593.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

8 publications found

Variant links:

Genes affected

GPCPD1 (HGNC:26957): (glycerophosphocholine phosphodiesterase 1) Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

GPCPD1 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPCPD1	NM_019593.5 link	c.1395+19A>G		intron_variant	Intron 16 of 19	ENST00000379019.7	NP_062539.1	Q9NPB8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPCPD1	ENST00000379019.7 link	c.1395+19A>G		intron_variant	Intron 16 of 19	1	NM_019593.5	ENSP00000368305.4		Q9NPB8

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37424

AN:

152074

Hom.:

5052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.232

GnomAD2 exomes

AF:

0.223

AC:

55385

AN:

247996

AF XY:

0.222

show subpopulations

Gnomad AFR exome

AF:

0.340

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.438

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.207

AC:

255699

AN:

1235860

Hom.:

28107

Cov.:

AF XY:

0.207

AC XY:

129458

AN XY:

625818

show subpopulations

African (AFR)

AF:

0.329

AC:

9467

AN:

28800

American (AMR)

AF:

0.153

AC:

6714

AN:

43840

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

4885

AN:

24708

East Asian (EAS)

AF:

0.382

AC:

14618

AN:

38276

South Asian (SAS)

AF:

0.197

AC:

15898

AN:

80798

European-Finnish (FIN)

AF:

0.195

AC:

10303

AN:

52722

Middle Eastern (MID)

AF:

0.235

AC:

1256

AN:

5336

European-Non Finnish (NFE)

AF:

0.199

AC:

181056

AN:

908790

Other (OTH)

AF:

0.219

AC:

11502

AN:

52590

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

8643

17285

25928

34570

43213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5874

11748

17622

23496

29370

<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:

0.246

AC:

37488

AN:

152194

Hom.:

5069

Cov.:

AF XY:

0.243

AC XY:

18100

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.335

AC:

13890

AN:

41496

American (AMR)

AF:

0.194

AC:

2974

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

668

AN:

3472

East Asian (EAS)

AF:

0.427

AC:

2210

AN:

5178

South Asian (SAS)

AF:

0.207

AC:

1001

AN:

4826

European-Finnish (FIN)

AF:

0.181

AC:

1922

AN:

10600

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.207

AC:

14082

AN:

68008

Other (OTH)

AF:

0.239

AC:

505

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1392

2784

4177

5569

6961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<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:

0.223

Hom.:

3364

Bravo

AF:

0.254

Asia WGS

AF:

0.326

AC:

1131

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.57

(source)

DANN

Benign

0.44

PhyloP100

-1.6

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)

0.010

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