dbSNP rs9701: PURB:c.*4809C>T (chr7-44879601-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.662

Variant links:

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]

PURB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
PURB	NM_033224.5 link	c.*4809C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000395699.5	NP_150093.1	Q96QR8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PURB	ENST00000395699 link	c.*4809C>T		3_prime_UTR_variant	Exon 1 of 1		NM_033224.5	ENSP00000379051.2		Q96QR8

Frequencies

GnomAD3 genomes

AF:

0.766

AC:

116191

AN:

151752

Hom.:

46758

Cov.:

show subpopulations

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.:

AF XY:

0.919

AC XY:

237

AN XY:

258

show subpopulations

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.:

AF XY:

0.759

AC XY:

56333

AN XY:

74220

show subpopulations

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over