Variant chr1-230357055-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001258311.2(PGBD5):c.598G>A(p.Ala200Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00624 in 1,614,130 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 81 hom. )

Consequence

PGBD5
NM_001258311.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.03

Variant links:

Genes affected

PGBD5 (HGNC:19405): (piggyBac transposable element derived 5) 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. [provided by RefSeq, May 2010]

PGBD5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008564383).

BP6

Variant 1-230357055-C-T is Benign according to our data. Variant chr1-230357055-C-T is described in ClinVar as [Benign]. Clinvar id is 770863.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00518 (788/152238) while in subpopulation SAS AF= 0.0203 (98/4816). AF 95% confidence interval is 0.0171. There are 4 homozygotes in gnomad4. There are 415 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGBD5	NM_001258311.2 linkuse as main transcript	c.598G>A	p.Ala200Thr	missense_variant	2/7	ENST00000391860.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGBD5	ENST00000391860.7 linkuse as main transcript	c.598G>A	p.Ala200Thr	missense_variant	2/7	1	NM_001258311.2	P1	Q8N414-1
PGBD5	ENST00000525115.1 linkuse as main transcript	c.391G>A	p.Ala131Thr	missense_variant	2/7	2			Q8N414-2

Frequencies

GnomAD3 genomes

AF:

0.00517

AC:

786

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.00717

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00701

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00651

AC:

1637

AN:

251364

Hom.:

AF XY:

0.00760

AC XY:

1032

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00295

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0197

Gnomad FIN exome

AF:

0.00656

Gnomad NFE exome

AF:

0.00615

Gnomad OTH exome

AF:

0.00701

GnomAD4 exome

AF:

0.00635

AC:

9283

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00686

AC XY:

4992

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00288

Gnomad4 ASJ exome

AF:

0.00302

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.00760

Gnomad4 NFE exome

AF:

0.00578

Gnomad4 OTH exome

AF:

0.00566

GnomAD4 genome

AF:

0.00518

AC:

788

AN:

152238

Hom.:

Cov.:

AF XY:

0.00558

AC XY:

415

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0203

Gnomad4 FIN

AF:

0.00717

Gnomad4 NFE

AF:

0.00700

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00560

Hom.:

Bravo

AF:

0.00391

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00593

AC:

ExAC

AF:

0.00679

AC:

824

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Uncertain

0.030

CADD

Uncertain

DANN

Pathogenic

1.0

Eigen

Uncertain

0.54

Eigen_PC

Uncertain

0.55

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

D;D

MetaRNN

Benign

0.0086

T;T

MetaSVM

Benign

-1.2

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.64

REVEL

Uncertain

0.36

Vest4

0.82

MVP

0.20

MPC

1.0

ClinPred

0.025

GERP RS

6.0

Varity_R

0.44

gMVP

0.62

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