rs9701

chr7-44879601-G-A

Variant summary

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

The NM_033224.5(PURB):c.*4809C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,300 control chromosomes in the GnomAD database, including 46,962 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 0.77 (46784 hom., cov: 29)
  • Exomes 𝑓: 0.91 (178 hom.)
• Consequence: PURB NM_033224.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

Genes affected

PURB (HGNC:9702): (purine rich element binding protein B) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PURB	NM_033224.5	c.*4809C>T		3_prime_UTR_variant	1/1	ENST00000395699.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PURB	ENST00000395699.5	c.*4809C>T		3_prime_UTR_variant	1/1		NM_033224.5	P1

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116191 AN: 151752 Hom.: 46758 Cov.: 29

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.907 AC: 392 AN: 432 Hom.: 178 Cov.: 0 AF XY: 0.919 AC XY: 237 AN XY: 258

Gnomad4 FIN exome AF: 0.908

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.766 AC: 116269 AN: 151868 Hom.: 46784 Cov.: 29 AF XY: 0.759 AC XY: 56333 AN XY: 74220

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.787

Alfa AF: 0.864 Hom.: 32637

Bravo AF: 0.740

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	11
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9701; hg19: chr7-44919200; COSMIC: COSV67480255; COSMIC: COSV67480255;