rs755662

chr20-5569972-A-T

Variant summary

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

The NM_019593.5(GPCPD1):c.1149+175T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,922 control chromosomes in the GnomAD database, including 22,680 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 0.54 (22680 hom., cov: 31)
• Consequence: GPCPD1 NM_019593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPCPD1	NM_019593.5	c.1149+175T>A		intron_variant		ENST00000379019.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPCPD1	ENST00000379019.7	c.1149+175T>A		intron_variant		1	NM_019593.5	P1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82512 AN: 151804 Hom.: 22649 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.544 AC: 82585 AN: 151922 Hom.: 22680 Cov.: 31 AF XY: 0.542 AC XY: 40250 AN XY: 74244

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.550

Alfa AF: 0.543 Hom.: 2854

Bravo AF: 0.541

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.27
Dann	Benign	0.43

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: rs755662; hg19: chr20-5550618;