chr6-24494235-G-A

Variant names:

• chr6-24494235-G-A
• rs16889393
• ENST00000474784.5:n.239+732C>T

Variant summary

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

The ENST00000474784.5(GPLD1):​n.239+732C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 152,238 control chromosomes in the GnomAD database, including 112 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 0.029 (112 hom., cov: 33)
• Consequence: GPLD1 ENST00000474784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.0906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000474784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPLD1	ENST00000474784.5	TSL:5	n.239+732C>T		intron	N/A
	GPLD1	ENST00000475417.1	TSL:3	n.233+732C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0293 AC: 4463 AN: 152120 Hom.: 111 Cov.: 33

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0294 AC: 4473 AN: 152238 Hom.: 112 Cov.: 33 AF XY: 0.0298 AC XY: 2220 AN XY: 74434

African (AFR) AF: 0.0237 AC: 985 AN: 41542

American (AMR) AF: 0.0279 AC: 427 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.0838 AC: 434 AN: 5180

South Asian (SAS) AF: 0.0979 AC: 472 AN: 4820

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0252 AC: 1714 AN: 68028

Other (OTH) AF: 0.0375 AC: 79 AN: 2108

Alfa AF: 0.0250 Hom.: 73

Bravo AF: 0.0293

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.75
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs16889393; hg19: chr6-24494463;