Variant 20-5578575-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000379019.7(GPCPD1):c.510C>T(p.Asp170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00986 in 1,612,208 control chromosomes in the GnomAD database, including 147 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0093 ( 13 hom., cov: 32)

Exomes 𝑓: 0.0099 ( 134 hom. )

Consequence

GPCPD1
ENST00000379019.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.74

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 20-5578575-G-A is Benign according to our data. Variant chr20-5578575-G-A is described in ClinVar as [Benign]. Clinvar id is 780073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.74 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 13 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPCPD1	NM_019593.5 linkuse as main transcript	c.510C>T	p.Asp170=	synonymous_variant	8/20	ENST00000379019.7	NP_062539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
GPCPD1	ENST00000379019.7 linkuse as main transcript	c.510C>T	p.Asp170=	synonymous_variant	8/20	1	NM_019593.5	ENSP00000368305	P1
GPCPD1	ENST00000481038.5 linkuse as main transcript	n.1918C>T		non_coding_transcript_exon_variant	3/15	2
GPCPD1	ENST00000481690.2 linkuse as main transcript	c.*128C>T		3_prime_UTR_variant, NMD_transcript_variant	7/8	3		ENSP00000488635

Frequencies

GnomAD3 genomes

AF:

0.00930

AC:

1415

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.0379

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0128

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00977

AC:

2457

AN:

251394

Hom.:

AF XY:

0.00957

AC XY:

1300

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00217

Gnomad ASJ exome

AF:

0.000198

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00425

Gnomad FIN exome

AF:

0.0397

Gnomad NFE exome

AF:

0.0115

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.00992

AC:

14480

AN:

1459978

Hom.:

134

Cov.:

AF XY:

0.00990

AC XY:

7191

AN XY:

726420

show subpopulations

Gnomad4 AFR exome

AF:

0.00132

Gnomad4 AMR exome

AF:

0.00221

Gnomad4 ASJ exome

AF:

0.000345

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00394

Gnomad4 FIN exome

AF:

0.0381

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.00900

GnomAD4 genome

AF:

0.00930

AC:

1415

AN:

152230

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

777

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00321

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00415

Gnomad4 FIN

AF:

0.0379

Gnomad4 NFE

AF:

0.0128

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00943

Hom.:

Bravo

AF:

0.00575

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00905

EpiControl

AF:

0.00765

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.083

DANN

Benign

0.26

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over