7-44879601-G-A

Variant names:

• chr7-44879601-G-A
• rs9701
• NM_033224.5:c.*4809C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

H2AZ2-DT (HGNC:52775): (H2AZ2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033224.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURB	NM_033224.5	MANE Select	c.*4809C>T		3_prime_UTR	Exon 1 of 1	NP_150093.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURB	ENST00000395699.5	TSL:6 MANE Select	c.*4809C>T		3_prime_UTR	Exon 1 of 1	ENSP00000379051.2
	H2AZ2-DT	ENST00000817614.1		n.242-1790G>A		intron	N/A
	H2AZ2-DT	ENST00000817615.1		n.306-1790G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.908 AC: 387 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

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

African (AFR) AF: 0.586 AC: 24238 AN: 41334

American (AMR) AF: 0.710 AC: 10832 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3152 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5152

South Asian (SAS) AF: 0.675 AC: 3246 AN: 4808

European-Finnish (FIN) AF: 0.896 AC: 9458 AN: 10556

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.902 AC: 61342 AN: 67990

Other (OTH) AF: 0.787 AC: 1650 AN: 2096

Alfa AF: 0.843 Hom.: 44958

Bravo AF: 0.740

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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