rs6922313

Positions:

• chr6-24438491-C-T

Variant summary

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

The NM_001503.4(GPLD1):​c.2021-1202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,086 control chromosomes in the GnomAD database, including 6,331 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 0.28 (6331 hom., cov: 33)
• Consequence: GPLD1 NM_001503.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPLD1	NM_001503.4	c.2021-1202G>A		intron_variant		ENST00000230036.2	NP_001494.2
GPLD1	XM_017010753.3	c.2051-1202G>A		intron_variant			XP_016866242.1
GPLD1	XM_047418657.1	c.1532-1202G>A		intron_variant			XP_047274613.1
GPLD1	XR_007059240.1	n.2328-1202G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPLD1	ENST00000230036.2	c.2021-1202G>A		intron_variant		1	NM_001503.4	ENSP00000230036	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42297 AN: 151968 Hom.: 6324 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.278 AC: 42332 AN: 152086 Hom.: 6331 Cov.: 33 AF XY: 0.272 AC XY: 20233 AN XY: 74336

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.246

Alfa AF: 0.279 Hom.: 1358

Bravo AF: 0.285

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.81

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: rs6922313; hg19: chr6-24438719;