ENST00000783087.1:n.*87C>G

Variant names:

• chr9-6413939-G-C
• NM_152896.3:c.153+296G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000783087.1(ENSG00000301961):​n.88C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000301961 ENST00000783087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 0 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]

ENSG00000301961 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783087.1. 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
	UHRF2	NM_152896.3	MANE Select	c.153+296G>C		intron	N/A	NP_690856.1
	UHRF2	NR_046386.2		n.445+296G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UHRF2	ENST00000276893.10	TSL:1 MANE Select	c.153+296G>C		intron	N/A	ENSP00000276893.5
	UHRF2	ENST00000468435.7	TSL:1	n.153+296G>C		intron	N/A	ENSP00000434182.1
	ENSG00000301961	ENST00000783087.1		n.88C>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 99192 Hom.: 0 Cov.: 1 AF XY: 0.00 AC XY: 0 AN XY: 50038

African (AFR) AF: 0.00 AC: 0 AN: 3294

American (AMR) AF: 0.00 AC: 0 AN: 2582

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3974

East Asian (EAS) AF: 0.00 AC: 0 AN: 8706

South Asian (SAS) AF: 0.00 AC: 0 AN: 1680

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6752

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 608

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64680

Other (OTH) AF: 0.00 AC: 0 AN: 6916

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.32
PhyloP100		-0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr9-6413939;