rs6053520

Variant names:

• chr20-5588016-T-C
• rs6053520
• NM_019593.5:c.232-1747A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019593.5(GPCPD1):​c.232-1747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,108 control chromosomes in the GnomAD database, including 5,442 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 0.26 (5442 hom., cov: 32)
• Consequence: GPCPD1 NM_019593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019593.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPCPD1	NM_019593.5	MANE Select	c.232-1747A>G		intron	N/A	NP_062539.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPCPD1	ENST00000379019.7	TSL:1 MANE Select	c.232-1747A>G		intron	N/A	ENSP00000368305.4
	GPCPD1	ENST00000718343.1		c.232-1747A>G		intron	N/A	ENSP00000520780.1
	GPCPD1	ENST00000481690.2	TSL:3	n.232-3694A>G		intron	N/A	ENSP00000488635.1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39337 AN: 151988 Hom.: 5425 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.259 AC: 39398 AN: 152108 Hom.: 5442 Cov.: 32 AF XY: 0.255 AC XY: 18992 AN XY: 74358

African (AFR) AF: 0.335 AC: 13888 AN: 41486

American (AMR) AF: 0.204 AC: 3119 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2213 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1114 AN: 4826

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10570

Middle Eastern (MID) AF: 0.221 AC: 64 AN: 290

European-Non Finnish (NFE) AF: 0.229 AC: 15581 AN: 67978

Other (OTH) AF: 0.248 AC: 524 AN: 2114

Alfa AF: 0.242 Hom.: 765

Bravo AF: 0.266

Asia WGS AF: 0.333 AC: 1157 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6053520; hg19: chr20-5568662;