rs1883415

chr6-24491247-A-C

Variant summary

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

The XM_017010753.3(GPLD1):c.45-1750T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,996 control chromosomes in the GnomAD database, including 8,991 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 0.34 (8991 hom., cov: 32)
• Consequence: GPLD1 XM_017010753.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

GPLD1 (HGNC:4459): (glycosylphosphatidylinositol specific phospholipase D1) Many proteins are tethered to the extracellular face of eukaryotic plasma membranes by a glycosylphosphatidylinositol (GPI) anchor. The GPI-anchor is a glycolipid found on many blood cells. The protein encoded by this gene is a GPI degrading enzyme. Glycosylphosphatidylinositol specific phospholipase D1 hydrolyzes the inositol phosphate linkage in proteins anchored by phosphatidylinositol glycans, thereby releasing the attached protein from the plasma membrane. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPLD1	XM_017010753.3	c.45-1750T>G		intron_variant
GPLD1	XM_047418658.1	c.45-1750T>G		intron_variant
GPLD1	XR_007059240.1	n.322-1750T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPLD1	ENST00000474784.5	n.240-1750T>G		intron_variant, non_coding_transcript_variant		5
GPLD1	ENST00000475417.1	n.234-1750T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51189 AN: 151878 Hom.: 8977 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.337 AC: 51253 AN: 151996 Hom.: 8991 Cov.: 32 AF XY: 0.330 AC XY: 24503 AN XY: 74290

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.312

Alfa AF: 0.334 Hom.: 16970

Bravo AF: 0.332

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.46
Dann	Benign	0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1883415; hg19: chr6-24491475;