rs8024695

Variant names:

• chr15-55347107-T-C
• rs8024695
• NM_004855.5:c.1124-3592T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004855.5(PIGB):​c.1124-3592T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,300 control chromosomes in the GnomAD database, including 2,279 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 0.15 (2279 hom., cov: 33)
• Consequence: PIGB NM_004855.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 9 publications found

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]

CCPG1 (HGNC:24227): (cell cycle progression 1) Involved in positive regulation of cell cycle and positive regulation of cell population proliferation. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGB	NM_004855.5	c.1124-3592T>C		intron_variant	Intron 9 of 11	ENST00000164305.10	NP_004846.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGB	ENST00000164305.10	c.1124-3592T>C		intron_variant	Intron 9 of 11	1	NM_004855.5	ENSP00000164305.5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22385 AN: 152182 Hom.: 2278 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0650

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.147 AC: 22386 AN: 152300 Hom.: 2279 Cov.: 33 AF XY: 0.153 AC XY: 11413 AN XY: 74482

African (AFR) AF: 0.129 AC: 5353 AN: 41560

American (AMR) AF: 0.216 AC: 3310 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2771 AN: 5174

South Asian (SAS) AF: 0.258 AC: 1248 AN: 4832

European-Finnish (FIN) AF: 0.124 AC: 1317 AN: 10610

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7512 AN: 68038

Other (OTH) AF: 0.158 AC: 333 AN: 2114

Alfa AF: 0.121 Hom.: 1087

Bravo AF: 0.156

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8024695; hg19: chr15-55639305;