ENST00000339382.3:c.865-10126G>A

Variant names:

• chr8-31006823-C-T
• rs11775287
• ENST00000339382.3:c.865-10126G>A

Variant summary

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

The ENST00000339382.3(PURG):​c.865-10126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,114 control chromosomes in the GnomAD database, including 13,031 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 (13031 hom., cov: 32)
• Consequence: PURG ENST00000339382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 4 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=-0.91).
• 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.865-10126G>A		intron_variant	Intron 1 of 1		NP_001015508.1
PURG	NM_001323312.2	c.865-10126G>A		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.865-10126G>A		intron_variant	Intron 1 of 1	1		ENSP00000345168.2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57969 AN: 151996 Hom.: 13027 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.381 AC: 57970 AN: 152114 Hom.: 13031 Cov.: 32 AF XY: 0.386 AC XY: 28667 AN XY: 74356

African (AFR) AF: 0.139 AC: 5758 AN: 41520

American (AMR) AF: 0.411 AC: 6278 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3600 AN: 5182

South Asian (SAS) AF: 0.329 AC: 1587 AN: 4824

European-Finnish (FIN) AF: 0.537 AC: 5673 AN: 10570

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

European-Non Finnish (NFE) AF: 0.470 AC: 31937 AN: 67958

Other (OTH) AF: 0.391 AC: 824 AN: 2110

Alfa AF: 0.429 Hom.: 39290

Bravo AF: 0.367

Asia WGS AF: 0.464 AC: 1609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.63
PhyloP100		-0.81
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: rs11775287; hg19: chr8-30864339;