rs6107653

Positions:

• chr20-5561825-C-A
• chr20-5561825-C-G

Variant summary

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

The NM_019593.5(GPCPD1):​c.1330-295G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,162 control chromosomes in the GnomAD database, including 1,854 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 0.15 (1854 hom., cov: 33)
• Consequence: GPCPD1 NM_019593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPCPD1	NM_019593.5	c.1330-295G>T		intron_variant		ENST00000379019.7	NP_062539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPCPD1	ENST00000379019.7	c.1330-295G>T		intron_variant		1	NM_019593.5	ENSP00000368305	P1
GPCPD1	ENST00000418646.5	c.307-3006G>T		intron_variant		5		ENSP00000396720
GPCPD1	ENST00000633552.1	c.*173-295G>T		intron_variant, NMD_transcript_variant		5		ENSP00000487616
GPCPD1	ENST00000481038.5	n.2738-295G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22518 AN: 152044 Hom.: 1853 Cov.: 33

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.148 AC: 22526 AN: 152162 Hom.: 1854 Cov.: 33 AF XY: 0.149 AC XY: 11104 AN XY: 74374

Gnomad4 AFR AF: 0.0916

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.150

Alfa AF: 0.168 Hom.: 2616

Bravo AF: 0.145

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.77

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: rs6107653; hg19: chr20-5542471;