Variant 6-28300890-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_032507.4(PGBD1):c.1036G>A(p.Asp346Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,614,108 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 22 hom. )

Consequence

PGBD1
NM_032507.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.10

Variant links:

Genes affected

PGBD1 (HGNC:19398): (piggyBac transposable element derived 1) The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families. This gene product is specifically expressed in the brain, however, its exact function is not known. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, May 2010]

PGBD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006383151).

BP6

Variant 6-28300890-G-A is Benign according to our data. Variant chr6-28300890-G-A is described in ClinVar as [Benign]. Clinvar id is 773194.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGBD1	NM_032507.4 linkuse as main transcript	c.1036G>A	p.Asp346Asn	missense_variant	7/7	ENST00000682144.1	NP_115896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGBD1	ENST00000682144.1 linkuse as main transcript	c.1036G>A	p.Asp346Asn	missense_variant	7/7		NM_032507.4	ENSP00000506997	P1
PGBD1	ENST00000259883.3 linkuse as main transcript	c.1036G>A	p.Asp346Asn	missense_variant	7/7	1		ENSP00000259883	P1

Frequencies

GnomAD3 genomes

AF:

0.00452

AC:

687

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000652

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0131

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0130

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00426

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00477

AC:

1198

AN:

250978

Hom.:

AF XY:

0.00442

AC XY:

600

AN XY:

135636

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.0103

Gnomad ASJ exome

AF:

0.00805

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000686

Gnomad FIN exome

AF:

0.0121

Gnomad NFE exome

AF:

0.00392

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00382

AC:

5579

AN:

1461878

Hom.:

Cov.:

AF XY:

0.00380

AC XY:

2767

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.0120

Gnomad4 ASJ exome

AF:

0.00815

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000730

Gnomad4 FIN exome

AF:

0.00975

Gnomad4 NFE exome

AF:

0.00363

Gnomad4 OTH exome

AF:

0.00325

GnomAD4 genome

AF:

0.00455

AC:

693

AN:

152230

Hom.:

Cov.:

AF XY:

0.00533

AC XY:

397

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.000650

Gnomad4 AMR

AF:

0.0135

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0130

Gnomad4 NFE

AF:

0.00426

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00418

Hom.:

Bravo

AF:

0.00414

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00430

AC:

ExAC

AF:

0.00410

AC:

498

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00365

EpiControl

AF:

0.00296

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2024	PGBD1: BS1, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 13, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.67

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.028

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Benign

0.65

LIST_S2

Benign

0.78

MetaRNN

Benign

0.0064

MetaSVM

Benign

-0.77

MutationAssessor

Uncertain

2.4

MutationTaster

Benign

0.99

N;N

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-0.65

REVEL

Benign

0.077

Sift

Uncertain

0.0090

Sift4G

Uncertain

0.049

Polyphen

0.98

Vest4

0.22

MVP

0.37

ClinPred

0.018

GERP RS

4.5

Varity_R

0.085

gMVP

0.28

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