chr8-31030446-G-A

Variant names:

• chr8-31030446-G-A
• rs2251621
• ENST00000339382.3:c.864+1473C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000339382.3(PURG):​c.864+1473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0571 in 152,040 control chromosomes in the GnomAD database, including 525 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 0.057 (525 hom., cov: 32)
• Consequence: PURG ENST00000339382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PURG	NM_001015508.3	c.864+1473C>T		intron_variant	Intron 1 of 1		NP_001015508.1
PURG	NM_001323312.2	c.864+1473C>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.864+1473C>T		intron_variant	Intron 1 of 1	1		ENSP00000345168.2

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8663 AN: 151922 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0278

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0571 AC: 8674 AN: 152040 Hom.: 525 Cov.: 32 AF XY: 0.0612 AC XY: 4544 AN XY: 74306

African (AFR) AF: 0.0134 AC: 558 AN: 41536

American (AMR) AF: 0.150 AC: 2294 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0278 AC: 96 AN: 3458

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5182

South Asian (SAS) AF: 0.131 AC: 631 AN: 4826

European-Finnish (FIN) AF: 0.0483 AC: 511 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0473 AC: 3213 AN: 67870

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0538 Hom.: 611

Bravo AF: 0.0642

Asia WGS AF: 0.177 AC: 612 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.86
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: rs2251621; hg19: chr8-30887962;