rs10971677

Variant names:

• chr9-33750239-C-T
• rs10971677
• ENST00000705030.1:n.644-11823G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_170201.1(UBE2R2-AS1):​n.370-11823G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,082 control chromosomes in the GnomAD database, including 4,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4686 hom., cov: 32)
• Consequence: UBE2R2-AS1 NR_170201.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0140
• Publications: 6 publications found

Genes affected

UBE2R2-AS1 (HGNC:49911): (UBE2R2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 9-33750239-C-T is Benign according to our data. Variant chr9-33750239-C-T is described in ClinVar as Benign. ClinVar VariationId is 1249985.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_170201.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2R2-AS1	NR_170201.1		n.370-11823G>A		intron	N/A
	UBE2R2-AS1	NR_170202.1		n.559-11823G>A		intron	N/A
	UBE2R2-AS1	NR_170203.1		n.560-11823G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2R2-AS1	ENST00000705030.1		n.644-11823G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37218 AN: 151964 Hom.: 4677 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.245 AC: 37244 AN: 152082 Hom.: 4686 Cov.: 32 AF XY: 0.243 AC XY: 18059 AN XY: 74348

African (AFR) AF: 0.279 AC: 11557 AN: 41474

American (AMR) AF: 0.234 AC: 3568 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5168

South Asian (SAS) AF: 0.118 AC: 569 AN: 4816

European-Finnish (FIN) AF: 0.280 AC: 2968 AN: 10590

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15693 AN: 67974

Other (OTH) AF: 0.241 AC: 509 AN: 2108

Alfa AF: 0.232 Hom.: 1875

Bravo AF: 0.250

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.63
PhyloP100		-0.014
PromoterAI		0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10971677; hg19: chr9-33750237;