Variant chr16-574101-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_004204.5(PIGQ):c.27G>A(p.Thr9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 1,607,878 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 30 hom., cov: 34)

Exomes 𝑓: 0.029 ( 714 hom. )

Consequence

PIGQ
NM_004204.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.69

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 16-574101-G-A is Benign according to our data. Variant chr16-574101-G-A is described in ClinVar as [Benign]. Clinvar id is 456041.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.69 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0193 (2940/152324) while in subpopulation NFE AF= 0.0317 (2155/68026). AF 95% confidence interval is 0.0306. There are 30 homozygotes in gnomad4. There are 1342 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 30 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGQ	NM_004204.5 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/11	ENST00000321878.10
PIGQ	NM_148920.4 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGQ	ENST00000321878.10 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/11	1	NM_004204.5	P1	Q9BRB3-2

Frequencies

GnomAD3 genomes

AF:

0.0193

AC:

2941

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00644

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0165

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.00584

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0317

Gnomad OTH

AF:

0.0220

GnomAD3 exomes

AF:

0.0194

AC:

4759

AN:

244746

Hom.:

AF XY:

0.0193

AC XY:

2564

AN XY:

133106

show subpopulations

Gnomad AFR exome

AF:

0.00518

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.0384

Gnomad EAS exome

AF:

0.0000547

Gnomad SAS exome

AF:

0.00351

Gnomad FIN exome

AF:

0.00872

Gnomad NFE exome

AF:

0.0317

Gnomad OTH exome

AF:

0.0219

GnomAD4 exome

AF:

0.0292

AC:

42479

AN:

1455554

Hom.:

714

Cov.:

AF XY:

0.0284

AC XY:

20596

AN XY:

723956

show subpopulations

Gnomad4 AFR exome

AF:

0.00512

Gnomad4 AMR exome

AF:

0.0117

Gnomad4 ASJ exome

AF:

0.0385

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.00358

Gnomad4 FIN exome

AF:

0.00969

Gnomad4 NFE exome

AF:

0.0347

Gnomad4 OTH exome

AF:

0.0247

GnomAD4 genome

AF:

0.0193

AC:

2940

AN:

152324

Hom.:

Cov.:

AF XY:

0.0180

AC XY:

1342

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00642

Gnomad4 AMR

AF:

0.0165

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00310

Gnomad4 FIN

AF:

0.00584

Gnomad4 NFE

AF:

0.0317

Gnomad4 OTH

AF:

0.0218

Alfa

AF:

0.0273

Hom.:

Bravo

AF:

0.0198

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0274

EpiControl

AF:

0.0298

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Epilepsy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

1.0

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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