Variant chr9-33750455-A-ACACAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NR_170204.1(UBE2R2-AS1):n.559-12040_559-12039insCTGTG 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 0.363 in 1,541,724 control chromosomes in the GnomAD database, including 105,900 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 15426 hom., cov: 0)

Exomes 𝑓: 0.36 ( 90474 hom. )

Consequence

UBE2R2-AS1
NR_170204.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.463

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 -10 ACMG points.

BP6

Variant 9-33750455-A-ACACAG is Benign according to our data. Variant chr9-33750455-A-ACACAG is described in ClinVar as [Benign]. Clinvar id is 1257582.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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.559-12040_559-12039insCTGTG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.644-12040_644-12039insCTGTG		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.432

AC:

65386

AN:

151492

Hom.:

15390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.644

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.355

AC:

493652

AN:

1390114

Hom.:

90474

Cov.:

AF XY:

0.352

AC XY:

241681

AN XY:

686048

show subpopulations

Gnomad4 AFR exome

AF:

0.669

Gnomad4 AMR exome

AF:

0.348

Gnomad4 ASJ exome

AF:

0.390

Gnomad4 EAS exome

AF:

0.241

Gnomad4 SAS exome

AF:

0.287

Gnomad4 FIN exome

AF:

0.388

Gnomad4 NFE exome

AF:

0.352

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

AF:

0.432

AC:

65479

AN:

151610

Hom.:

15426

Cov.:

AF XY:

0.429

AC XY:

31757

AN XY:

74078

show subpopulations

Gnomad4 AFR

AF:

0.644

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.395

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.412

Alfa

AF:

0.414

Hom.:

1472

Bravo

AF:

0.442

Asia WGS

AF:

0.309

AC:

1073

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

Jun 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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