rs2744575
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The XM_017010753.3(GPLD1):c.44+220G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 361,032 control chromosomes in the GnomAD database, including 20,384 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.34 ( 8971 hom., cov: 32)
Exomes 𝑓: 0.32 ( 11413 hom. )
Consequence
GPLD1
XM_017010753.3 intron
XM_017010753.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.140
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 6-24494747-C-G is Benign according to our data. Variant chr6-24494747-C-G is described in ClinVar as [Benign]. Clinvar id is 1281626.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPLD1 | XM_017010753.3 | c.44+220G>C | intron_variant | ||||
GPLD1 | XM_047418658.1 | c.44+220G>C | intron_variant | ||||
GPLD1 | XR_007059240.1 | n.321+220G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPLD1 | ENST00000474784.5 | n.239+220G>C | intron_variant, non_coding_transcript_variant | 5 | |||||
GPLD1 | ENST00000475417.1 | n.233+220G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.337 AC: 51137AN: 151964Hom.: 8957 Cov.: 32
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GnomAD4 exome AF: 0.320 AC: 66930AN: 208952Hom.: 11413 AF XY: 0.319 AC XY: 33794AN XY: 105792
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GnomAD4 genome ? AF: 0.337 AC: 51200AN: 152080Hom.: 8971 Cov.: 32 AF XY: 0.329 AC XY: 24487AN XY: 74352
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at