rs6107653

Variant names:

• chr20-5561825-C-A
• rs6107653
• NM_019593.5:c.1330-295G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000379019.7(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 ENST00000379019.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379019.7. 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.1330-295G>T		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.1330-295G>T		intron	N/A	ENSP00000368305.4
	GPCPD1	ENST00000718343.1		c.1330-295G>T		intron	N/A	ENSP00000520780.1
	GPCPD1	ENST00000418646.5	TSL:5	c.306-3006G>T		intron	N/A	ENSP00000396720.1

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

African (AFR) AF: 0.0916 AC: 3806 AN: 41530

American (AMR) AF: 0.165 AC: 2519 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3472

East Asian (EAS) AF: 0.0517 AC: 268 AN: 5182

South Asian (SAS) AF: 0.125 AC: 604 AN: 4830

European-Finnish (FIN) AF: 0.157 AC: 1665 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12429 AN: 67974

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.166 Hom.: 3262

Bravo AF: 0.145

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6107653; hg19: chr20-5542471;