rs6053520

Positions:

• chr20-5588016-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPCPD1	NM_019593.5	c.232-1747A>G		intron_variant		ENST00000379019.7	NP_062539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPCPD1	ENST00000379019.7	c.232-1747A>G		intron_variant		1	NM_019593.5	ENSP00000368305	P1
GPCPD1	ENST00000481690.2	c.232-3694A>G		intron_variant, NMD_transcript_variant		3		ENSP00000488635

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

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.248

Alfa AF: 0.239 Hom.: 718

Bravo AF: 0.266

Asia WGS AF: 0.333 AC: 1157 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs6053520; hg19: chr20-5568662;