chr6-24430830-G-T

Variant names:

• chr6-24430830-G-T
• rs793687
• NM_001503.4:c.2437-1712C>A

Variant summary

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

The NM_001503.4(GPLD1):​c.2437-1712C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,944 control chromosomes in the GnomAD database, including 28,992 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 0.61 (28992 hom., cov: 32)
• Consequence: GPLD1 NM_001503.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPLD1	NM_001503.4	c.2437-1712C>A		intron_variant	Intron 24 of 24	ENST00000230036.2	NP_001494.2
GPLD1	XM_017010753.3	c.2467-1712C>A		intron_variant	Intron 25 of 25		XP_016866242.1
GPLD1	XM_047418657.1	c.1948-1712C>A		intron_variant	Intron 19 of 19		XP_047274613.1
GPLD1	XR_007059240.1	n.2744-1712C>A		intron_variant	Intron 25 of 26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPLD1	ENST00000230036.2	c.2437-1712C>A		intron_variant	Intron 24 of 24	1	NM_001503.4	ENSP00000230036.1
GPLD1	ENST00000492917.2	n.312-1712C>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92869 AN: 151826 Hom.: 28988 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.611 AC: 92901 AN: 151944 Hom.: 28992 Cov.: 32 AF XY: 0.604 AC XY: 44860 AN XY: 74246

African (AFR) AF: 0.564 AC: 23381 AN: 41422

American (AMR) AF: 0.563 AC: 8592 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2493 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1271 AN: 5160

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4820

European-Finnish (FIN) AF: 0.585 AC: 6153 AN: 10520

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46329 AN: 67984

Other (OTH) AF: 0.605 AC: 1276 AN: 2110

Alfa AF: 0.647 Hom.: 4183

Bravo AF: 0.606

Asia WGS AF: 0.396 AC: 1377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.75
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs793687; hg19: chr6-24431058;