Variant chr10-114959784-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_139169.5(TRUB1):c.500G>A(p.Arg167Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,598,310 control chromosomes in the GnomAD database, including 173,175 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.51 ( 22028 hom., cov: 32)

Exomes 𝑓: 0.45 ( 151147 hom. )

Consequence

TRUB1
NM_139169.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Variant links:

Genes affected

TRUB1 (HGNC:16060): (TruB pseudouridine synthase family member 1) 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]

TRUB1 links:

TRUB1 (HGNC:):

TRUB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRUB1	NM_139169.5 linkuse as main transcript	c.500G>A	p.Arg167Lys	missense_variant	4/8	ENST00000298746.5	NP_631908.1	Q8WWH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRUB1	ENST00000298746.5 linkuse as main transcript	c.500G>A	p.Arg167Lys	missense_variant	4/8	1	NM_139169.5	ENSP00000298746.3		Q8WWH5
TRUB1	ENST00000485065.1 linkuse as main transcript	n.368G>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77564

AN:

151916

Hom.:

21986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.0362

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.423

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.522

GnomAD3 exomes

AF:

0.412

AC:

102998

AN:

250164

Hom.:

24289

AF XY:

0.413

AC XY:

55876

AN XY:

135252

show subpopulations

Gnomad AFR exome

AF:

0.751

Gnomad AMR exome

AF:

0.247

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.0391

Gnomad SAS exome

AF:

0.413

Gnomad FIN exome

AF:

0.431

Gnomad NFE exome

AF:

0.459

Gnomad OTH exome

AF:

0.439

GnomAD4 exome

AF:

0.446

AC:

644705

AN:

1446276

Hom.:

151147

Cov.:

AF XY:

0.444

AC XY:

320084

AN XY:

720288

show subpopulations

Gnomad4 AFR exome

AF:

0.747

Gnomad4 AMR exome

AF:

0.263

Gnomad4 ASJ exome

AF:

0.520

Gnomad4 EAS exome

AF:

0.0320

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.436

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.447

GnomAD4 genome

AF:

0.511

AC:

77659

AN:

152034

Hom.:

22028

Cov.:

AF XY:

0.502

AC XY:

37293

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.749

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.535

Gnomad4 EAS

AF:

0.0363

Gnomad4 SAS

AF:

0.402

Gnomad4 FIN

AF:

0.423

Gnomad4 NFE

AF:

0.457

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.474

Hom.:

32929

Bravo

AF:

0.512

TwinsUK

AF:

0.460

AC:

1706

ALSPAC

AF:

0.472

AC:

1819

ESP6500AA

AF:

0.739

AC:

3254

ESP6500EA

AF:

0.461

AC:

3964

ExAC

AF:

0.424

AC:

51522

Asia WGS

AF:

0.290

AC:

1009

AN:

3478

EpiCase

AF:

0.466

EpiControl

AF:

0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.55

DEOGEN2

Benign

0.020

Eigen

Benign

-0.83

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.055

LIST_S2

Benign

0.024

MetaRNN

Benign

0.0000012

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-0.35

PrimateAI

Uncertain

0.52

PROVEAN

Benign

0.84

REVEL

Benign

0.085

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.0090

MPC

0.28

ClinPred

0.0064

GERP RS

4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.039

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.31

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.31

Position offset: 1

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