dbSNP rs2240116: PIGO:c.512-17C>T (chr9-35094376-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_032634.4(PIGO):c.512-17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 1,594,534 control chromosomes in the GnomAD database, including 5,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.067 ( 601 hom., cov: 32)

Exomes 𝑓: 0.059 ( 4862 hom. )

Consequence

PIGO
NM_032634.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.49

Variant links:

Genes affected

PIGO (HGNC:23215): (phosphatidylinositol glycan anchor biosynthesis class O) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid which contains three mannose molecules in its core backbone. The GPI-anchor is found on many blood cells and serves to anchor proteins to the cell surface. This protein is involved in the transfer of ethanolaminephosphate (EtNP) to the third mannose in GPI. At least three alternatively spliced transcripts encoding two distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

PIGO links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 9-35094376-G-A is Benign according to our data. Variant chr9-35094376-G-A is described in ClinVar as [Benign]. Clinvar id is 262100.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGO	NM_032634.4 link	c.512-17C>T		intron_variant	Intron 2 of 10	ENST00000378617.4	NP_116023.2	Q8TEQ8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGO	ENST00000378617.4 link	c.512-17C>T		intron_variant	Intron 2 of 10	1	NM_032634.4	ENSP00000367880.3		Q8TEQ8-1

Frequencies

GnomAD3 genomes

AF:

0.0672

AC:

10224

AN:

152152

Hom.:

600

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0570

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.0794

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0758

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0445

Gnomad OTH

AF:

0.0702

GnomAD3 exomes

AF:

0.0898

AC:

20753

AN:

231066

Hom.:

1655

AF XY:

0.0876

AC XY:

11002

AN XY:

125662

show subpopulations

Gnomad AFR exome

AF:

0.0530

Gnomad AMR exome

AF:

0.137

Gnomad ASJ exome

AF:

0.0822

Gnomad EAS exome

AF:

0.335

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.0761

Gnomad NFE exome

AF:

0.0433

Gnomad OTH exome

AF:

0.0737

GnomAD4 exome

AF:

0.0591

AC:

85191

AN:

1442264

Hom.:

4862

Cov.:

AF XY:

0.0612

AC XY:

43908

AN XY:

717684

show subpopulations

Gnomad4 AFR exome

AF:

0.0575

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.0880

Gnomad4 EAS exome

AF:

0.345

Gnomad4 SAS exome

AF:

0.117

Gnomad4 FIN exome

AF:

0.0772

Gnomad4 NFE exome

AF:

0.0399

Gnomad4 OTH exome

AF:

0.0719

GnomAD4 genome

AF:

0.0672

AC:

10227

AN:

152270

Hom.:

601

Cov.:

AF XY:

0.0715

AC XY:

5322

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0569

Gnomad4 AMR

AF:

0.0796

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.0758

Gnomad4 NFE

AF:

0.0445

Gnomad4 OTH

AF:

0.0695

Alfa

AF:

0.0513

Hom.:

120

Bravo

AF:

0.0714

Asia WGS

AF:

0.188

AC:

653

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Jan 09, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hyperphosphatasia with intellectual disability syndrome 2

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.76

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