8-31006823-C-T

Position:

• chr8-31006823-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001015508.3(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 NM_001015508.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PURG	NM_001015508.3	c.865-10126G>A		intron_variant			NP_001015508.1
PURG	NM_001323312.2	c.865-10126G>A		intron_variant			NP_001310241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PURG	ENST00000339382.3	c.865-10126G>A		intron_variant		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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.391

Alfa AF: 0.453 Hom.: 26074

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11775287; hg19: chr8-30864339;