rs3800324

Variant names:

• chr6-28296904-G-A
• rs3800324
• NM_032507.4:c.731G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-28296904-G-A
• chr6-28296904-G-C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_032507.4(PGBD1):​c.731G>A​(p.Gly244Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 1,613,996 control chromosomes in the GnomAD database, including 5,597 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.085 (774 hom., cov: 32)
  • Exomes 𝑓: 0.061 (4823 hom.)
• Consequence: PGBD1 NM_032507.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 37 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGBD1	NM_032507.4	MANE Select	c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	NP_115896.1	Q96JS3
	PGBD1	NM_001184743.2		c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	NP_001171672.1	Q96JS3
	PGBD1	NM_001386059.1		c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	NP_001372988.1	Q96JS3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGBD1	ENST00000682144.1	MANE Select	c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	ENSP00000506997.1	Q96JS3
	PGBD1	ENST00000259883.3	TSL:1	c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	ENSP00000259883.3	Q96JS3
	PGBD1	ENST00000918204.1		c.731G>A	p.Gly244Glu	missense	Exon 5 of 7	ENSP00000588263.1

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12867 AN: 152110 Hom.: 771 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0750

GnomAD2 exomes AF: 0.0926 AC: 23281 AN: 251288 AF XY: 0.0907

Gnomad AFR exome AF: 0.114

Gnomad AMR exome AF: 0.131

Gnomad ASJ exome AF: 0.0663

Gnomad EAS exome AF: 0.307

Gnomad FIN exome AF: 0.0515

Gnomad NFE exome AF: 0.0471

Gnomad OTH exome AF: 0.0665

GnomAD4 exome AF: 0.0613 AC: 89633 AN: 1461766 Hom.: 4823 Cov.: 31 AF XY: 0.0632 AC XY: 45947 AN XY: 727198

African (AFR) AF: 0.114 AC: 3827 AN: 33464

American (AMR) AF: 0.128 AC: 5721 AN: 44706

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 1617 AN: 26136

East Asian (EAS) AF: 0.321 AC: 12728 AN: 39692

South Asian (SAS) AF: 0.123 AC: 10649 AN: 86250

European-Finnish (FIN) AF: 0.0510 AC: 2725 AN: 53420

Middle Eastern (MID) AF: 0.0850 AC: 490 AN: 5766

European-Non Finnish (NFE) AF: 0.0431 AC: 47934 AN: 1111944

Other (OTH) AF: 0.0653 AC: 3942 AN: 60388

GnomAD4 genome AF: 0.0846 AC: 12885 AN: 152230 Hom.: 774 Cov.: 32 AF XY: 0.0864 AC XY: 6428 AN XY: 74434

African (AFR) AF: 0.115 AC: 4758 AN: 41540

American (AMR) AF: 0.116 AC: 1777 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 208 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1597 AN: 5180

South Asian (SAS) AF: 0.126 AC: 608 AN: 4822

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3135 AN: 68012

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0600 Hom.: 1773

Bravo AF: 0.0915

TwinsUK AF: 0.0369 AC: 137

ALSPAC AF: 0.0436 AC: 168

ESP6500AA AF: 0.113 AC: 498

ESP6500EA AF: 0.0476 AC: 409

ExAC AF: 0.0903 AC: 10963

Asia WGS AF: 0.123 AC: 427 AN: 3478

EpiCase AF: 0.0442

EpiControl AF: 0.0462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.80	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.96
DEOGEN2	Benign	0.0031	T
Eigen	Benign	-0.94
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.019	N
LIST_S2	Benign	0.42	T
MetaRNN	Benign	0.0045	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.1	L
PhyloP100		-0.074
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.071
Sift	Benign	0.13	T
Sift4G	Benign	0.18	T
Polyphen		0.0070	B
Vest4		0.041
ClinPred		0.00057	T
GERP RS		0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.081
gMVP		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.23		Position offset: -4

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

Other links and lift over

dbSNP: rs3800324; hg19: chr6-28264681; COSMIC: COSV52551663;