9-33750239-C-T

Position:

• chr9-33750239-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_170204.1(UBE2R2-AS1):​n.559-11823G>A variant causes a intron, non coding transcript 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_170204.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2R2-AS1	NR_170204.1	n.559-11823G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1	n.644-11823G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.241

Alfa AF: 0.230 Hom.: 1643

Bravo AF: 0.250

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10971677; hg19: chr9-33750237;