8-31007428-C-A

Variant names:

• chr8-31007428-C-A
• rs1362911
• ENST00000339382.3:c.865-10731G>T

Variant summary

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

The ENST00000339382.3(PURG):​c.865-10731G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,956 control chromosomes in the GnomAD database, including 7,165 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 0.22 (7165 hom., cov: 32)
• Consequence: PURG ENST00000339382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PURG	NM_001015508.3	c.865-10731G>T		intron_variant	Intron 1 of 1		NP_001015508.1
PURG	NM_001323312.2	c.865-10731G>T		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.865-10731G>T		intron_variant	Intron 1 of 1	1		ENSP00000345168.2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33080 AN: 151840 Hom.: 7137 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0955

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.218 AC: 33168 AN: 151956 Hom.: 7165 Cov.: 32 AF XY: 0.213 AC XY: 15785 AN XY: 74274

African (AFR) AF: 0.565 AC: 23379 AN: 41404

American (AMR) AF: 0.139 AC: 2118 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 127 AN: 3438

East Asian (EAS) AF: 0.178 AC: 918 AN: 5170

South Asian (SAS) AF: 0.0952 AC: 458 AN: 4812

European-Finnish (FIN) AF: 0.0547 AC: 578 AN: 10572

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5152 AN: 67966

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.104 Hom.: 2695

Bravo AF: 0.239

Asia WGS AF: 0.185 AC: 641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.50
PhyloP100		-0.16
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: rs1362911; hg19: chr8-30864944;