chr9-33799372-T-C

Position:

• chr9-33799372-T-C

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.373+411A>G 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 0.663 in 577,094 control chromosomes in the GnomAD database, including 121,044 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.66 (29270 hom., cov: 33)
  • Exomes 𝑓: 0.66 (91774 hom.)
• Consequence: UBE2R2-AS1 NR_170204.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.85

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=-1.0).
• BP6: Variant 9-33799372-T-C is Benign according to our data. Variant chr9-33799372-T-C is described in ClinVar as [Benign]. Clinvar id is 1246185.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2R2-AS1	NR_170204.1	n.373+411A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1	n.235+415A>G		intron_variant, non_coding_transcript_variant
UBE2R2-AS1	ENST00000454429.2	n.296+415A>G		intron_variant, non_coding_transcript_variant		5
UBE2R2-AS1	ENST00000668091.1	n.1295+415A>G		intron_variant, non_coding_transcript_variant
UBE2R2-AS1	ENST00000669609.1	n.1400+415A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.656 AC: 94317 AN: 143682 Hom.: 29238 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.578

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.657

GnomAD4 exome AF: 0.665 AC: 287962 AN: 433292 Hom.: 91774 AF XY: 0.665 AC XY: 148804 AN XY: 223738

Gnomad4 AFR exome AF: 0.642

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.617

Gnomad4 EAS exome AF: 0.773

Gnomad4 SAS exome AF: 0.722

Gnomad4 FIN exome AF: 0.677

Gnomad4 NFE exome AF: 0.646

Gnomad4 OTH exome AF: 0.659

GnomAD4 genome AF: 0.656 AC: 94403 AN: 143802 Hom.: 29270 Cov.: 33 AF XY: 0.660 AC XY: 46347 AN XY: 70270

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.657

Alfa AF: 0.616 Hom.: 58784

Asia WGS AF: 0.693 AC: 2411 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

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs216345; hg19: chr9-33799370;