6-28300890-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
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
NM_032507.4 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 3.10
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 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_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00452 AC: 687AN: 152112Hom.: 5 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
687
AN:
152112
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00477 AC: 1198AN: 250978 AF XY: 0.00442 show subpopulations
GnomAD2 exomes
AF:
AC:
1198
AN:
250978
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00382 AC: 5579AN: 1461878Hom.: 22 Cov.: 35 AF XY: 0.00380 AC XY: 2767AN XY: 727242 show subpopulations
GnomAD4 exome
AF:
AC:
5579
AN:
1461878
Hom.:
Cov.:
35
AF XY:
AC XY:
2767
AN XY:
727242
Gnomad4 AFR exome
AF:
AC:
16
AN:
33480
Gnomad4 AMR exome
AF:
AC:
536
AN:
44720
Gnomad4 ASJ exome
AF:
AC:
213
AN:
26136
Gnomad4 EAS exome
AF:
AC:
0
AN:
39698
Gnomad4 SAS exome
AF:
AC:
63
AN:
86258
Gnomad4 FIN exome
AF:
AC:
521
AN:
53418
Gnomad4 NFE exome
AF:
AC:
4033
AN:
1112004
Gnomad4 Remaining exome
AF:
AC:
196
AN:
60396
Heterozygous variant carriers
0
366
733
1099
1466
1832
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
146
292
438
584
730
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.00455 AC: 693AN: 152230Hom.: 6 Cov.: 32 AF XY: 0.00533 AC XY: 397AN XY: 74430 show subpopulations
GnomAD4 genome
AF:
AC:
693
AN:
152230
Hom.:
Cov.:
32
AF XY:
AC XY:
397
AN XY:
74430
Gnomad4 AFR
AF:
AC:
0.000650195
AN:
0.000650195
Gnomad4 AMR
AF:
AC:
0.0134729
AN:
0.0134729
Gnomad4 ASJ
AF:
AC:
0.00605187
AN:
0.00605187
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.000207039
AN:
0.000207039
Gnomad4 FIN
AF:
AC:
0.0130164
AN:
0.0130164
Gnomad4 NFE
AF:
AC:
0.00426383
AN:
0.00426383
Gnomad4 OTH
AF:
AC:
0.0047259
AN:
0.0047259
Heterozygous variant carriers
0
39
78
118
157
196
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
14
ALSPAC
AF:
AC:
19
ESP6500AA
AF:
AC:
1
ESP6500EA
AF:
AC:
37
ExAC
AF:
AC:
498
Asia WGS
AF:
AC:
3
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Sep 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
PGBD1: BS1, BS2 -
Dec 13, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Mutation Taster
=100/0
polymorphism
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at