Variant 9-33799372-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.85

Variant links:

Genes affected

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

UBE2R2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 linkuse as main transcript	n.373+411A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.235+415A>G	intron_variant, non_coding_transcript_variant
UBE2R2-AS1	ENST00000454429.2 linkuse as main transcript	n.296+415A>G	intron_variant, non_coding_transcript_variant	5
UBE2R2-AS1	ENST00000668091.1 linkuse as main transcript	n.1295+415A>G	intron_variant, non_coding_transcript_variant
UBE2R2-AS1	ENST00000669609.1 linkuse as main transcript	n.1400+415A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.656

AC:

94317

AN:

143682

Hom.:

29238

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.660

AC XY:

46347

AN XY:

70270

show subpopulations

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

LINK: link

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over