6-28289600-T-C

Variant names:

• chr6-28289600-T-C
• rs13211507
• NM_032507.4:c.642+2432T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032507.4(PGBD1):​c.642+2432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.062 in 152,264 control chromosomes in the GnomAD database, including 374 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 0.062 (374 hom., cov: 32)
• Consequence: PGBD1 NM_032507.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 57 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032507.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGBD1	NM_032507.4	MANE Select	c.642+2432T>C		intron	N/A	NP_115896.1
	PGBD1	NM_001184743.2		c.642+2432T>C		intron	N/A	NP_001171672.1
	PGBD1	NM_001386059.1		c.642+2432T>C		intron	N/A	NP_001372988.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGBD1	ENST00000682144.1	MANE Select	c.642+2432T>C		intron	N/A	ENSP00000506997.1
	PGBD1	ENST00000259883.3	TSL:1	c.642+2432T>C		intron	N/A	ENSP00000259883.3

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9445 AN: 152146 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0620 AC: 9441 AN: 152264 Hom.: 374 Cov.: 32 AF XY: 0.0562 AC XY: 4182 AN XY: 74468

African (AFR) AF: 0.0557 AC: 2316 AN: 41554

American (AMR) AF: 0.0275 AC: 421 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.0398 AC: 422 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 6007 AN: 68014

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0786 Hom.: 1195

Bravo AF: 0.0616

Asia WGS AF: 0.00577 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.2
DANN	Benign	0.96
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13211507; hg19: chr6-28257377;