chr16-579119-G-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP3BP4_StrongBP6_Moderate
The NM_004204.5(PIGQ):c.1274G>T(p.Arg425Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000352 in 1,612,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00057 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
PIGQ
NM_004204.5 missense
NM_004204.5 missense
Scores
6
4
9
Clinical Significance
Conservation
PhyloP100: 8.07
Genes affected
PIGQ (HGNC:14135): (phosphatidylinositol glycan anchor biosynthesis class Q) This gene is involved in the first step in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This gene encodes a N-acetylglucosaminyl transferase component that is part of the complex that catalyzes transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Multiple lines of computational evidence support a deleterious effect 8: AlphaMissense, BayesDel_noAF, Cadd, Eigen, FATHMM_MKL, phyloP100way_vertebrate, PrimateAI, PROVEAN [when BayesDel_addAF, max_spliceai, M_CAP, MetaRNN, MutationAssessor, MutationTaster was below the threshold]
BP4
Computational evidence support a benign effect (MetaRNN=0.026449978).
BP6
Variant 16-579119-G-T is Benign according to our data. Variant chr16-579119-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 526295.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGQ | NM_004204.5 | c.1274G>T | p.Arg425Leu | missense_variant | 7/11 | ENST00000321878.10 | NP_004195.2 | |
PIGQ | NM_148920.4 | c.1274G>T | p.Arg425Leu | missense_variant | 7/10 | NP_683721.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.1274G>T | p.Arg425Leu | missense_variant | 7/11 | 1 | NM_004204.5 | ENSP00000326674.6 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000611 AC: 153AN: 250276Hom.: 0 AF XY: 0.000597 AC XY: 81AN XY: 135632
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GnomAD4 exome AF: 0.000330 AC: 482AN: 1460664Hom.: 0 Cov.: 31 AF XY: 0.000330 AC XY: 240AN XY: 726664
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GnomAD4 genome AF: 0.000565 AC: 86AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000834 AC XY: 62AN XY: 74346
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 22, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;D
Sift4G
Benign
T;T;D;D
Polyphen
D;D;D;.
Vest4
MVP
MPC
0.66
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at