20-5607803-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019593.5(GPCPD1):c.-29+3039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 148,322 control chromosomes in the GnomAD database, including 37,019 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 0.70 (37019 hom., cov: 23)
• Consequence: GPCPD1 NM_019593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPCPD1	NM_019593.5	c.-29+3039T>C		intron_variant		ENST00000379019.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPCPD1	ENST00000379019.7	c.-29+3039T>C		intron_variant		1	NM_019593.5	P1
GPCPD1	ENST00000481690.2	c.-29+3039T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.695 AC: 103074 AN: 148220 Hom.: 36976 Cov.: 23

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.680

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.696 AC: 103163 AN: 148322 Hom.: 37019 Cov.: 23 AF XY: 0.689 AC XY: 49719 AN XY: 72176

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.685

Alfa AF: 0.848 Hom.: 16622

Bravo AF: 0.715

Asia WGS AF: 0.670 AC: 2327 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.7
Dann	Benign	0.63

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

Other links and lift over

dbSNP: rs238295; hg19: chr20-5588449;