rs1883415

Variant names:

• chr6-24491247-A-C
• rs1883415
• ENST00000474784.5:n.240-1750T>G

Variant summary

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

The ENST00000474784.5(GPLD1):​n.240-1750T>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 ENST00000474784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPLD1	XM_017010753.3	c.45-1750T>G		intron_variant	Intron 1 of 25		XP_016866242.1
GPLD1	XM_047418658.1	c.45-1750T>G		intron_variant	Intron 1 of 17		XP_047274614.1
GPLD1	XR_007059240.1	n.322-1750T>G		intron_variant	Intron 1 of 26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPLD1	ENST00000474784.5	n.240-1750T>G		intron_variant	Intron 1 of 10	5
GPLD1	ENST00000475417.1	n.234-1750T>G		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.381 AC: 15777 AN: 41440

American (AMR) AF: 0.231 AC: 3535 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1006 AN: 5176

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3508 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23917 AN: 67958

Other (OTH) AF: 0.312 AC: 656 AN: 2104

Alfa AF: 0.336 Hom.: 22433

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1883415; hg19: chr6-24491475;