ENST00000339382.3:c.865-166A>G

Variant names:

• chr8-30996863-T-C
• rs17648656
• ENST00000339382.3:c.865-166A>G

Variant summary

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

The ENST00000339382.3(PURG):​c.865-166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,648 control chromosomes in the GnomAD database, including 13,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.39 (13145 hom., cov: 31)
• Consequence: PURG ENST00000339382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000339382.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURG	NM_001015508.3		c.865-166A>G		intron	N/A	NP_001015508.1
	PURG	NM_001323312.2		c.865-166A>G		intron	N/A	NP_001310241.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURG	ENST00000339382.3	TSL:1	c.865-166A>G		intron	N/A	ENSP00000345168.2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58723 AN: 151530 Hom.: 13142 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.387 AC: 58732 AN: 151648 Hom.: 13145 Cov.: 31 AF XY: 0.392 AC XY: 29070 AN XY: 74144

African (AFR) AF: 0.159 AC: 6581 AN: 41494

American (AMR) AF: 0.416 AC: 6339 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1734 AN: 3454

East Asian (EAS) AF: 0.697 AC: 3608 AN: 5176

South Asian (SAS) AF: 0.330 AC: 1594 AN: 4824

European-Finnish (FIN) AF: 0.536 AC: 5659 AN: 10558

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

European-Non Finnish (NFE) AF: 0.471 AC: 31828 AN: 67600

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.405 Hom.: 2326

Bravo AF: 0.374

Asia WGS AF: 0.467 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		0.96
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: rs17648656; hg19: chr8-30854379;