1-230357055-C-T
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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
NM_001258311.2 missense
Scores
2
6
5
Clinical Significance
Conservation
PhyloP100: 6.03
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]
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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 | 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 | c.598G>A | p.Ala200Thr | missense_variant | 2/7 | 1 | NM_001258311.2 | P1 | |
PGBD5 | ENST00000525115.1 | c.391G>A | p.Ala131Thr | missense_variant | 2/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00517 AC: 786AN: 152120Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00651 AC: 1637AN: 251364Hom.: 25 AF XY: 0.00760 AC XY: 1032AN XY: 135872
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GnomAD4 exome AF: 0.00635 AC: 9283AN: 1461892Hom.: 81 Cov.: 31 AF XY: 0.00686 AC XY: 4992AN XY: 727246
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GnomAD4 genome AF: 0.00518 AC: 788AN: 152238Hom.: 4 Cov.: 32 AF XY: 0.00558 AC XY: 415AN XY: 74438
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
REVEL
Uncertain
Vest4
0.82
MVP
MPC
1.0
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at