rs12032643

Positions:

• chr1-248874237-G-A
• chr1-248874237-G-C
• chr1-248874237-G-T

Variant summary

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

The XM_011544161.4(PGBD2):​c.-48+345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,128 control chromosomes in the GnomAD database, including 1,846 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 0.14 (1846 hom., cov: 32)
• Consequence: PGBD2 XM_011544161.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.43

Genes affected

PGBD2 (HGNC:19399): (piggyBac transposable element derived 2) 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. The exact function of this gene is not known. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGBD2	XM_011544161.4	c.-48+345G>A		intron_variant			XP_011542463.1
		n.248874237G>A		intergenic_region
TRE-CTC2-1	unassigned_transcript_321	c.-11G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21667 AN: 152010 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.143 AC: 21681 AN: 152128 Hom.: 1846 Cov.: 32 AF XY: 0.143 AC XY: 10669 AN XY: 74386

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0758

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0925 Hom.: 422

Bravo AF: 0.142

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0010
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12032643; hg19: chr1-249168436;