NM_004855.5:c.1527C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004855.5(PIGB):c.1527C>T(p.Ser509Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 1,601,842 control chromosomes in the GnomAD database, including 5,992 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1244 hom., cov: 32)

Exomes 𝑓: 0.074 ( 4748 hom. )

Consequence

PIGB
NM_004855.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.519

Publications

4 publications found

Variant links:

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]

PIGB links:

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 links:

DNAAF4-CCPG1 (HGNC:43019): (DNAAF4-CCPG1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring dyslexia susceptibility 1 candidate 1 (DYX1C1) and cell cycle progression 1 (CCPG1) genes on chromosome 15. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]

DNAAF4-CCPG1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 15-55355294-C-T is Benign according to our data. Variant chr15-55355294-C-T is described in ClinVar as [Benign]. Clinvar id is 1577109.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.519 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGB	NM_004855.5 link	c.1527C>T	p.Ser509Ser	synonymous_variant	Exon 12 of 12	ENST00000164305.10	NP_004846.4	Q92521
CCPG1	NM_001204450.2 link	c.*926G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000442196.8	NP_001191379.1	Q9ULG6-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGB	ENST00000164305.10 link	c.1527C>T	p.Ser509Ser	synonymous_variant	Exon 12 of 12	1	NM_004855.5	ENSP00000164305.5		Q92521
CCPG1	ENST00000442196.8 link	c.*926G>A		3_prime_UTR_variant	Exon 9 of 9	2	NM_001204450.2	ENSP00000403400.3		Q9ULG6-5

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16291

AN:

152062

Hom.:

1241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0778

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0572

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0708

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.0758

AC:

18560

AN:

244836

AF XY:

0.0778

show subpopulations

Gnomad AFR exome

AF:

0.209

Gnomad AMR exome

AF:

0.0441

Gnomad ASJ exome

AF:

0.108

Gnomad EAS exome

AF:

0.000337

Gnomad FIN exome

AF:

0.0520

Gnomad NFE exome

AF:

0.0716

Gnomad OTH exome

AF:

0.0742

GnomAD4 exome

AF:

0.0745

AC:

107969

AN:

1449662

Hom.:

4748

Cov.:

AF XY:

0.0756

AC XY:

54555

AN XY:

721440

show subpopulations

African (AFR)

AF:

0.212

AC:

6971

AN:

32936

American (AMR)

AF:

0.0485

AC:

2119

AN:

43660

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

2954

AN:

25866

East Asian (EAS)

AF:

0.000253

AC:

AN:

39580

South Asian (SAS)

AF:

0.112

AC:

9473

AN:

84948

European-Finnish (FIN)

AF:

0.0557

AC:

2970

AN:

53344

Middle Eastern (MID)

AF:

0.0985

AC:

565

AN:

5734

European-Non Finnish (NFE)

AF:

0.0707

AC:

78076

AN:

1103656

Other (OTH)

AF:

0.0806

AC:

4831

AN:

59938

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.453

Heterozygous variant carriers

3908

7815

11723

15630

19538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.107

AC:

16309

AN:

152180

Hom.:

1244

Cov.:

AF XY:

0.105

AC XY:

7809

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.206

AC:

8566

AN:

41490

American (AMR)

AF:

0.0776

AC:

1186

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

399

AN:

3472

East Asian (EAS)

AF:

0.00193

AC:

AN:

5184

South Asian (SAS)

AF:

0.101

AC:

485

AN:

4824

European-Finnish (FIN)

AF:

0.0572

AC:

606

AN:

10596

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0709

AC:

4820

AN:

68010

Other (OTH)

AF:

0.0999

AC:

211

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

721

1442

2162

2883

3604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0910

Hom.:

503

Bravo

AF:

0.110

Asia WGS

AF:

0.0470

AC:

163

AN:

3476

EpiCase

AF:

0.0760

EpiControl

AF:

0.0758

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

PIGB-related disorder

Benign:1

Nov 20, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as 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

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.3

(source)

DANN

Benign

0.84

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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NM_004855.5:c.1527C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over