rs12050587

chr15-55335330-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004855.5(PIGB):c.794+1323A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,070 control chromosomes in the GnomAD database, including 8,522 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8522 hom., cov: 32)
• Consequence: PIGB NM_004855.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGB	NM_004855.5	c.794+1323A>G		intron_variant		ENST00000164305.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGB	ENST00000164305.10	c.794+1323A>G		intron_variant		1	NM_004855.5	P2
PIGB	ENST00000539642.5	c.797+1323A>G		intron_variant		5		A2
PIGB	ENST00000565367.5	c.*30+1323A>G		intron_variant, NMD_transcript_variant		2
PIGB	ENST00000570059.1	c.*363+1323A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48195 AN: 151952 Hom.: 8509 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.317 AC: 48242 AN: 152070 Hom.: 8522 Cov.: 32 AF XY: 0.318 AC XY: 23657 AN XY: 74360

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.310

Alfa AF: 0.254 Hom.: 2396

Bravo AF: 0.332

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.16
Dann	Benign	0.64

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: rs12050587; hg19: chr15-55627528;