Variant 22-42615296-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NR_029422.2(RNU12):n.53C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00595 in 205,260 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0062 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0053 ( 2 hom. )

Consequence

RNU12
NR_029422.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.91

Variant links:

Genes affected

RNU12 (HGNC:19380): (RNA, U12 small nuclear)

RNU12 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNU12	NR_029422.2 linkuse as main transcript	n.53C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNU12	ENST00000362512.1 linkuse as main transcript	n.53C>T		non_coding_transcript_exon_variant	1/1
	ENST00000602478.1 linkuse as main transcript	n.53C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00620

AC:

944

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00526

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00386

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0141

Gnomad SAS

AF:

0.00332

Gnomad FIN

AF:

0.000943

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00804

Gnomad OTH

AF:

0.00335

GnomAD4 exome

AF:

0.00530

AC:

281

AN:

52984

Hom.:

Cov.:

AF XY:

0.00536

AC XY:

161

AN XY:

30012

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00543

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00422

Gnomad4 SAS exome

AF:

0.00338

Gnomad4 FIN exome

AF:

0.00215

Gnomad4 NFE exome

AF:

0.00668

Gnomad4 OTH exome

AF:

0.00538

GnomAD4 genome

AF:

0.00618

AC:

941

AN:

152276

Hom.:

Cov.:

AF XY:

0.00584

AC XY:

435

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00522

Gnomad4 AMR

AF:

0.00386

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0139

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.000943

Gnomad4 NFE

AF:

0.00803

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.000855

Hom.:

Bravo

AF:

0.00629

Asia WGS

AF:

0.0150

AC:

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

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

RNU12: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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