chr6-28283207-G-A

Position:

• chr6-28283207-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032507.4(PGBD1):​c.-38-569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,146 control chromosomes in the GnomAD database, including 2,486 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2486 hom., cov: 32)
• Consequence: PGBD1 NM_032507.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGBD1	NM_032507.4	c.-38-569G>A		intron_variant		ENST00000682144.1	NP_115896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGBD1	ENST00000682144.1	c.-38-569G>A		intron_variant			NM_032507.4	ENSP00000506997	P1
PGBD1	ENST00000259883.3	c.-58-549G>A		intron_variant		1		ENSP00000259883	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25341 AN: 152028 Hom.: 2481 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.146

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.167 AC: 25362 AN: 152146 Hom.: 2486 Cov.: 32 AF XY: 0.160 AC XY: 11905 AN XY: 74416

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.144

Alfa AF: 0.138 Hom.: 1443

Bravo AF: 0.181

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs6901575; hg19: chr6-28250984;