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GeneBe

20-5578575-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_019593.5(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
NM_019593.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.74 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 13 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPCPD1NM_019593.5 linkuse as main transcriptc.510C>T p.Asp170= synonymous_variant 8/20 ENST00000379019.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPCPD1ENST00000379019.7 linkuse as main transcriptc.510C>T p.Asp170= synonymous_variant 8/201 NM_019593.5 P1
GPCPD1ENST00000481038.5 linkuse as main transcriptn.1918C>T non_coding_transcript_exon_variant 3/152
GPCPD1ENST00000481690.2 linkuse as main transcriptc.*128C>T 3_prime_UTR_variant, NMD_transcript_variant 7/83

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00930
AC:
1415
AN:
152112
Hom.:
13
Cov.:
32
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.:
28
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.:
31
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00930
AC:
1415
AN:
152230
Hom.:
13
Cov.:
32
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.:
5
Bravo
AF:
0.00575
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00905
EpiControl
AF:
0.00765

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 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.

Other links and lift over

dbSNP: rs150734510; hg19: chr20-5559221; COSMIC: COSV100980159; COSMIC: COSV100980159; API