20-5607803-A-G

Variant names:

• chr20-5607803-A-G
• rs238295
• NM_019593.5:c.-29+3039T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPCPD1	NM_019593.5	c.-29+3039T>C		intron_variant	Intron 1 of 19	ENST00000379019.7	NP_062539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPCPD1	ENST00000379019.7	c.-29+3039T>C		intron_variant	Intron 1 of 19	1	NM_019593.5	ENSP00000368305.4
GPCPD1	ENST00000718343.1	c.-29+3039T>C		intron_variant	Intron 1 of 19			ENSP00000520780.1
GPCPD1	ENST00000481690.2	n.-29+3039T>C		intron_variant	Intron 1 of 7	3		ENSP00000488635.1

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

African (AFR) AF: 0.872 AC: 34833 AN: 39944

American (AMR) AF: 0.607 AC: 9038 AN: 14888

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2280 AN: 3454

East Asian (EAS) AF: 0.726 AC: 3629 AN: 5002

South Asian (SAS) AF: 0.633 AC: 2975 AN: 4698

European-Finnish (FIN) AF: 0.513 AC: 5074 AN: 9900

Middle Eastern (MID) AF: 0.703 AC: 201 AN: 286

European-Non Finnish (NFE) AF: 0.642 AC: 43140 AN: 67202

Other (OTH) AF: 0.685 AC: 1411 AN: 2060

Alfa AF: 0.917 Hom.: 35028

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs238295; hg19: chr20-5588449;