Variant rs11539570 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2

The NM_015679.3(TRUB2):c.60G>T(p.Gly20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.015 in 1,614,160 control chromosomes in the GnomAD database, including 216 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. Synonymous variant affecting the same amino acid position (i.e. G20G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0091 ( 5 hom., cov: 33)

Exomes 𝑓: 0.016 ( 211 hom. )

Consequence

TRUB2
NM_015679.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.334

Variant links:

Genes affected

TRUB2 (HGNC:17170): (TruB pseudouridine synthase family member 2) Pseudouridine is an abundant component of rRNAs and tRNAs and is enzymatically generated by isomerization of uridine by pseudouridine synthase (Zucchini et al., 2003 [PubMed 12736709]).[supplied by OMIM, Mar 2008]

TRUB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP7

Synonymous conserved (PhyloP=-0.334 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00913 (1390/152280) while in subpopulation SAS AF= 0.0189 (91/4820). AF 95% confidence interval is 0.0157. There are 5 homozygotes in gnomad4. There are 627 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TRUB2	NM_015679.3 linkuse as main transcript	c.60G>T	p.Gly20=	synonymous_variant	1/8	ENST00000372890.6
TRUB2	NM_001329861.2 linkuse as main transcript	c.60G>T	p.Gly20=	synonymous_variant	1/7
TRUB2	NM_001329863.2 linkuse as main transcript	c.-328G>T		5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRUB2	ENST00000372890.6 linkuse as main transcript	c.60G>T	p.Gly20=	synonymous_variant	1/8	1	NM_015679.3	P1	O95900-1
TRUB2	ENST00000460320.1 linkuse as main transcript	n.65G>T		non_coding_transcript_exon_variant	1/9	2

Frequencies

GnomAD3 genomes

AF:

0.00915

AC:

1393

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00246

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00727

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0191

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0148

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.0119

AC:

2990

AN:

251458

Hom.:

AF XY:

0.0131

AC XY:

1774

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00295

Gnomad AMR exome

AF:

0.00792

Gnomad ASJ exome

AF:

0.0115

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0204

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.0158

Gnomad OTH exome

AF:

0.0161

GnomAD4 exome

AF:

0.0156

AC:

22876

AN:

1461880

Hom.:

211

Cov.:

AF XY:

0.0159

AC XY:

11568

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00825

Gnomad4 ASJ exome

AF:

0.0113

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.00168

Gnomad4 NFE exome

AF:

0.0173

Gnomad4 OTH exome

AF:

0.0148

GnomAD4 genome

AF:

0.00913

AC:

1390

AN:

152280

Hom.:

Cov.:

AF XY:

0.00842

AC XY:

627

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00245

Gnomad4 AMR

AF:

0.00726

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0189

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.0148

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00383

Hom.:

Bravo

AF:

0.00978

EpiCase

AF:

0.0159

EpiControl

AF:

0.0146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

9.4

DANN

Benign

0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over