Variant chr15-55319235-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004855.5(PIGB):c.-16A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,597,260 control chromosomes in the GnomAD database, including 37,261 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4515 hom., cov: 32)

Exomes 𝑓: 0.20 ( 32746 hom. )

Consequence

PIGB
NM_004855.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.339

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 15-55319235-A-G is Benign according to our data. Variant chr15-55319235-A-G is described in ClinVar as [Benign]. Clinvar id is 1327019.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIGB	NM_004855.5 linkuse as main transcript	c.-16A>G		5_prime_UTR_variant	1/12	ENST00000164305.10	NP_004846.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGB	ENST00000164305.10 linkuse as main transcript	c.-16A>G		5_prime_UTR_variant	1/12	1	NM_004855.5	ENSP00000164305	P2

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34931

AN:

152058

Hom.:

4507

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.235

GnomAD3 exomes

AF:

0.242

AC:

53676

AN:

221532

Hom.:

7876

AF XY:

0.237

AC XY:

28443

AN XY:

120214

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.322

Gnomad ASJ exome

AF:

0.177

Gnomad EAS exome

AF:

0.575

Gnomad SAS exome

AF:

0.279

Gnomad FIN exome

AF:

0.178

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.223

GnomAD4 exome

AF:

0.201

AC:

289767

AN:

1445084

Hom.:

32746

Cov.:

AF XY:

0.201

AC XY:

144396

AN XY:

717112

show subpopulations

Gnomad4 AFR exome

AF:

0.268

Gnomad4 AMR exome

AF:

0.313

Gnomad4 ASJ exome

AF:

0.180

Gnomad4 EAS exome

AF:

0.527

Gnomad4 SAS exome

AF:

0.274

Gnomad4 FIN exome

AF:

0.174

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.230

AC:

34960

AN:

152176

Hom.:

4515

Cov.:

AF XY:

0.233

AC XY:

17297

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.270

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.290

Gnomad4 FIN

AF:

0.176

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.193

Hom.:

675

Bravo

AF:

0.241

Asia WGS

AF:

0.378

AC:

1315

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Developmental and epileptic encephalopathy, 80

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.4

DANN

Benign

0.63

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over