rs7020390

Variant names:

• chr9-6470921-A-G
• rs7020390
• NM_152896.3:c.864-4470A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-6470921-A-G
• chr9-6470921-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152896.3(UHRF2):​c.864-4470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,038 control chromosomes in the GnomAD database, including 25,382 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 0.56 (25382 hom., cov: 32)
• Consequence: UHRF2 NM_152896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• Publications: 6 publications found

Genes affected

UHRF2 (HGNC:12557): (ubiquitin like with PHD and ring finger domains 2) This gene encodes a nuclear protein which is involved in cell-cycle regulation. The encoded protein is a ubiquitin-ligase capable of ubiquinating PCNP (PEST-containing nuclear protein), and together they may play a role in tumorigenesis. The encoded protein contains an NIRF_N domain, a PHD finger, a set- and ring-associated (SRA) domain, and a RING finger domain and several of these domains have been shown to be essential for the regulation of cell proliferation. This protein may also have a role in intranuclear degradation of polyglutamine aggregates. Alternative splicing results in multiple transcript variants some of which are non-protein coding. [provided by RefSeq, Feb 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UHRF2	NM_152896.3	c.864-4470A>G		intron_variant	Intron 4 of 15	ENST00000276893.10	NP_690856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UHRF2	ENST00000276893.10	c.864-4470A>G		intron_variant	Intron 4 of 15	1	NM_152896.3	ENSP00000276893.5

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84757 AN: 151920 Hom.: 25321 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.558 AC: 84863 AN: 152038 Hom.: 25382 Cov.: 32 AF XY: 0.561 AC XY: 41666 AN XY: 74334

African (AFR) AF: 0.769 AC: 31874 AN: 41464

American (AMR) AF: 0.606 AC: 9246 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1845 AN: 5172

South Asian (SAS) AF: 0.441 AC: 2125 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5449 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31266 AN: 67958

Other (OTH) AF: 0.545 AC: 1153 AN: 2114

Alfa AF: 0.526 Hom.: 5989

Bravo AF: 0.574

Asia WGS AF: 0.413 AC: 1437 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.67
PhyloP100		-0.83
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: rs7020390; hg19: chr9-6470921; COSMIC: COSV52792731;