rs8024695

Positions:

• chr15-55347107-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

CCPG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PIGB	NM_004855.5	c.1124-3592T>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.1124-3592T>C		intron_variant		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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.158

Alfa AF: 0.122 Hom.: 780

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

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: rs8024695; hg19: chr15-55639305;