rs9467160

chr6-24441518-G-A

Variant summary

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

The NM_001503.4(GPLD1):c.2020+4028C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,054 control chromosomes in the GnomAD database, including 6,628 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 (6628 hom., cov: 32)
• Consequence: GPLD1 NM_001503.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPLD1	NM_001503.4	c.2020+4028C>T		intron_variant		ENST00000230036.2
GPLD1	XM_017010753.3	c.2050+4028C>T		intron_variant
GPLD1	XM_047418657.1	c.1531+4028C>T		intron_variant
GPLD1	XR_007059240.1	n.2327+4028C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPLD1	ENST00000230036.2	c.2020+4028C>T		intron_variant		1	NM_001503.4	P1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43112 AN: 151936 Hom.: 6619 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.284 AC: 43151 AN: 152054 Hom.: 6628 Cov.: 32 AF XY: 0.277 AC XY: 20623 AN XY: 74320

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.255

Alfa AF: 0.264 Hom.: 8397

Bravo AF: 0.291

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.3
Dann	Benign	0.84

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: rs9467160; hg19: chr6-24441746;