rs2290344

chr15-55327598-T-C

Variant summary

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

The NM_004855.5(PIGB):c.485T>C(p.Met162Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,610,112 control chromosomes in the GnomAD database, including 19,526 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.12 (1910 hom., cov: 32)
  • Exomes 𝑓: 0.13 (17616 hom.)
• Consequence: PIGB NM_004855.5 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.83

Genes affected

PIGB (HGNC:8959): (phosphatidylinositol glycan anchor biosynthesis class B) This gene encodes a transmembrane protein that is located in the endoplasmic reticulum and is involved in GPI-anchor biosynthesis. The glycosylphosphatidylinositol (GPI) anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This gene is thought to encode a member of a family of dolichol-phosphate-mannose (Dol-P-Man) dependent mannosyltransferases. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=8.1926584E-4).
• BP6: Variant 15-55327598-T-C is Benign according to our data. Variant chr15-55327598-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1585299.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGB	NM_004855.5	c.485T>C	p.Met162Thr	missense_variant	4/12	ENST00000164305.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGB	ENST00000164305.10	c.485T>C	p.Met162Thr	missense_variant	4/12	1	NM_004855.5	P2

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18164 AN: 152106 Hom.: 1911 Cov.: 32

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.136

GnomAD3 exomes AF: 0.176 AC: 43378 AN: 246248 Hom.: 6102 AF XY: 0.172 AC XY: 23050 AN XY: 133652

Gnomad AFR exome AF: 0.0315

Gnomad AMR exome AF: 0.277

Gnomad ASJ exome AF: 0.121

Gnomad EAS exome AF: 0.575

Gnomad SAS exome AF: 0.233

Gnomad FIN exome AF: 0.123

Gnomad NFE exome AF: 0.105

Gnomad OTH exome AF: 0.150

GnomAD4 exome AF: 0.130 AC: 189779 AN: 1457888 Hom.: 17616 Cov.: 30 AF XY: 0.132 AC XY: 95765 AN XY: 725268

Gnomad4 AFR exome AF: 0.0304

Gnomad4 AMR exome AF: 0.266

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.526

Gnomad4 SAS exome AF: 0.227

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.139

GnomAD4 genome AF: 0.119 AC: 18156 AN: 152224 Hom.: 1910 Cov.: 32 AF XY: 0.127 AC XY: 9417 AN XY: 74420

Gnomad4 AFR AF: 0.0357

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.135

Alfa AF: 0.123 Hom.: 4006

Bravo AF: 0.124

TwinsUK AF: 0.111 AC: 412

ALSPAC AF: 0.108 AC: 416

ESP6500AA AF: 0.0389 AC: 144

ESP6500EA AF: 0.108 AC: 889

ExAC AF: 0.169 AC: 20394

Asia WGS AF: 0.344 AC: 1199 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

PIGB-related condition Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 13, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.47	T
BayesDel_noAF	Benign	-0.31
Cadd	Benign	16
Dann	Benign	0.87
DEOGEN2	Benign	0.0031	T;T;T
Eigen	Benign	-0.58
Eigen_PC	Benign	-0.30
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.56	T;T;T
MetaRNN	Benign	0.00082	T;T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	0.035	N;.;.
MutationTaster	Benign	0.96	P;P
PrimateAI	Benign	0.40	T
PROVEAN	Benign	1.1	N;N;.
REVEL	Benign	0.22
Sift	Benign	0.33	T;T;.
Sift4G	Benign	0.34	T;T;T
Polyphen		0.0	B;.;.
Vest4		0.13
MPC		0.047
ClinPred		0.0032	T
GERP RS		3.2
Varity_R		0.060
gMVP		0.40

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: rs2290344; hg19: chr15-55619796; COSMIC: COSV51241438;