chr1-248874237-G-A

Variant names:

• chr1-248874237-G-A
• rs12032643
• XM_011544161.4:c.-48+345G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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]

TRE-CTC2-1 (HGNC:34978):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.211 AC: 8772 AN: 41484

American (AMR) AF: 0.0766 AC: 1172 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1832 AN: 5154

South Asian (SAS) AF: 0.110 AC: 531 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10578

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7174 AN: 68010

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.117 Hom.: 2546

Bravo AF: 0.142

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0010
DANN	Benign	0.77
PhyloP100		-7.4

Splicing

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

Other links and lift over

dbSNP: rs12032643; hg19: chr1-249168436;