Variant chr16-572565-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004204.5(PIGQ):c.-9-1501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 455,356 control chromosomes in the GnomAD database, including 53,024 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 16187 hom., cov: 33)

Exomes 𝑓: 0.48 ( 36837 hom. )

Consequence

PIGQ
NM_004204.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0170

Variant links:

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]

PIGQ links:

ENSG00000282907 (HGNC:):

ENSG00000282907 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 16-572565-A-G is Benign according to our data. Variant chr16-572565-A-G is described in ClinVar as [Benign]. Clinvar id is 1185510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGQ	NM_004204.5 link	c.-9-1501A>G		intron_variant	Intron 1 of 10	ENST00000321878.10	NP_004195.2	Q9BRB3-2B2RAU6
PIGQ	NM_148920.4 link	c.-9-1501A>G		intron_variant	Intron 1 of 9		NP_683721.1	Q9BRB3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGQ	ENST00000321878.10 link	c.-9-1501A>G		intron_variant	Intron 1 of 10	1	NM_004204.5	ENSP00000326674.6		Q9BRB3-2

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69171

AN:

151308

Hom.:

16155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.638

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.333

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.406

GnomAD3 exomes

AF:

0.495

AC:

63591

AN:

128376

Hom.:

16495

AF XY:

0.500

AC XY:

35130

AN XY:

70298

show subpopulations

Gnomad AFR exome

AF:

0.476

Gnomad AMR exome

AF:

0.547

Gnomad ASJ exome

AF:

0.372

Gnomad EAS exome

AF:

0.614

Gnomad SAS exome

AF:

0.622

Gnomad FIN exome

AF:

0.520

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.421

GnomAD4 exome

AF:

0.482

AC:

146510

AN:

303930

Hom.:

36837

Cov.:

AF XY:

0.493

AC XY:

85379

AN XY:

173046

show subpopulations

Gnomad4 AFR exome

AF:

0.485

Gnomad4 AMR exome

AF:

0.547

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.616

Gnomad4 SAS exome

AF:

0.619

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.422

Gnomad4 OTH exome

AF:

0.453

GnomAD4 genome

AF:

0.457

AC:

69255

AN:

151426

Hom.:

16187

Cov.:

AF XY:

0.466

AC XY:

34492

AN XY:

73998

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.479

Gnomad4 ASJ

AF:

0.375

Gnomad4 EAS

AF:

0.638

Gnomad4 SAS

AF:

0.628

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.412

Alfa

AF:

0.425

Hom.:

2492

Bravo

AF:

0.450

Asia WGS

AF:

0.661

AC:

2297

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jul 15, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 71% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 66. Only high quality variants are reported. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Developmental and epileptic encephalopathy, 77

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.9

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over