rs7183960

Positions:

• chr15-55330497-T-C
• chr15-55330497-T-G

Variant summary

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

The ENST00000164305.10(PIGB):​c.653+643T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,956 control chromosomes in the GnomAD database, including 8,732 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 (8732 hom., cov: 32)
• Consequence: PIGB ENST00000164305.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-0.97).
• 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	Protein	UniProt
PIGB	NM_004855.5	c.653+643T>C		intron_variant		ENST00000164305.10	NP_004846.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGB	ENST00000164305.10	c.653+643T>C		intron_variant		1	NM_004855.5	ENSP00000164305	P2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48930 AN: 151838 Hom.: 8719 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.322 AC: 48981 AN: 151956 Hom.: 8732 Cov.: 32 AF XY: 0.325 AC XY: 24148 AN XY: 74274

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.313

Alfa AF: 0.246 Hom.: 8221

Bravo AF: 0.333

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.32

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: rs7183960; hg19: chr15-55622695;