8-31006785-T-G

Variant names:

• chr8-31006785-T-G
• rs11779521
• ENST00000339382.3:c.865-10088A>C

Variant summary

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

The ENST00000339382.3(PURG):​c.865-10088A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,090 control chromosomes in the GnomAD database, including 13,004 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 0.38 (13004 hom., cov: 32)
• Consequence: PURG ENST00000339382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 5 publications found

Genes affected

PURG (HGNC:17930): (purine rich element binding protein G) The exact function of this gene is not known, however, its encoded product is highly similar to purine-rich element binding protein A. The latter is a DNA-binding protein which binds preferentially to the single strand of the purine-rich element termed PUR, and has been implicated in the control of both DNA replication and transcription. This gene lies in close proximity to the Werner syndrome gene, but on the opposite strand, on chromosome 8p11. [provided by RefSeq, Apr 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PURG	NM_001015508.3	c.865-10088A>C		intron_variant	Intron 1 of 1		NP_001015508.1
PURG	NM_001323312.2	c.865-10088A>C		intron_variant	Intron 2 of 2		NP_001310241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PURG	ENST00000339382.3	c.865-10088A>C		intron_variant	Intron 1 of 1	1		ENSP00000345168.2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57841 AN: 151972 Hom.: 13000 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.380 AC: 57841 AN: 152090 Hom.: 13004 Cov.: 32 AF XY: 0.385 AC XY: 28612 AN XY: 74338

African (AFR) AF: 0.136 AC: 5641 AN: 41516

American (AMR) AF: 0.413 AC: 6306 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3590 AN: 5168

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4824

European-Finnish (FIN) AF: 0.536 AC: 5654 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31925 AN: 67964

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.368 Hom.: 1785

Bravo AF: 0.366

Asia WGS AF: 0.463 AC: 1608 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.48
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11779521; hg19: chr8-30864301;