20-5561446-T-C

Position:

• chr20-5561446-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.1395+19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,388,054 control chromosomes in the GnomAD database, including 33,176 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 0.25 (5069 hom., cov: 33)
  • Exomes 𝑓: 0.21 (28107 hom.)
• Consequence: GPCPD1 NM_019593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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]

GPCPD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPCPD1	NM_019593.5	c.1395+19A>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.1395+19A>G		intron_variant		1	NM_019593.5	ENSP00000368305.4
GPCPD1	ENST00000418646.5	c.306-2627A>G		intron_variant		5		ENSP00000396720.1
GPCPD1	ENST00000481038.5	n.2803+19A>G		intron_variant		2
GPCPD1	ENST00000633552.1	n.*238+19A>G		intron_variant		5		ENSP00000487616.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37424 AN: 152074 Hom.: 5052 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.232

GnomAD3 exomes AF: 0.223 AC: 55385 AN: 247996 Hom.: 6930 AF XY: 0.222 AC XY: 29776 AN XY: 134078

Gnomad AFR exome AF: 0.340

Gnomad AMR exome AF: 0.148

Gnomad ASJ exome AF: 0.192

Gnomad EAS exome AF: 0.438

Gnomad SAS exome AF: 0.203

Gnomad FIN exome AF: 0.191

Gnomad NFE exome AF: 0.210

Gnomad OTH exome AF: 0.213

GnomAD4 exome AF: 0.207 AC: 255699 AN: 1235860 Hom.: 28107 Cov.: 17 AF XY: 0.207 AC XY: 129458 AN XY: 625818

Gnomad4 AFR exome AF: 0.329

Gnomad4 AMR exome AF: 0.153

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.382

Gnomad4 SAS exome AF: 0.197

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.199

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.246 AC: 37488 AN: 152194 Hom.: 5069 Cov.: 33 AF XY: 0.243 AC XY: 18100 AN XY: 74412

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.239

Alfa AF: 0.216 Hom.: 2269

Bravo AF: 0.254

Asia WGS AF: 0.326 AC: 1131 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.44
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2273372; hg19: chr20-5542092; COSMIC: COSV66830888;