16-580665-G-A

Position:

• chr16-580665-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000321878.10(PIGQ):​c.1417-193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 607,444 control chromosomes in the GnomAD database, including 69,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (16813 hom., cov: 33)
  • Exomes 𝑓: 0.47 (52800 hom.)
• Consequence: PIGQ ENST00000321878.10 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.49

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 16-580665-G-A is Benign according to our data. Variant chr16-580665-G-A is described in ClinVar as [Benign]. Clinvar id is 1281528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIGQ	NM_004204.5	c.1417-193G>A		intron_variant		ENST00000321878.10	NP_004195.2
PIGQ	NM_148920.4	c.1417-193G>A		intron_variant			NP_683721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGQ	ENST00000321878.10	c.1417-193G>A		intron_variant		1	NM_004204.5	ENSP00000326674	P1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70516 AN: 151992 Hom.: 16782 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.471 AC: 214581 AN: 455334 Hom.: 52800 Cov.: 0 AF XY: 0.478 AC XY: 115436 AN XY: 241248

Gnomad4 AFR exome AF: 0.494

Gnomad4 AMR exome AF: 0.523

Gnomad4 ASJ exome AF: 0.389

Gnomad4 EAS exome AF: 0.679

Gnomad4 SAS exome AF: 0.620

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.443

GnomAD4 genome AF: 0.464 AC: 70600 AN: 152110 Hom.: 16813 Cov.: 33 AF XY: 0.472 AC XY: 35120 AN XY: 74372

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.418

Alfa AF: 0.460 Hom.: 2047

Bravo AF: 0.457

Asia WGS AF: 0.662 AC: 2304 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs1981483; hg19: chr16-630665;