chr10-114975582-T-C

Position:

• chr10-114975582-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139169.5(TRUB1):​c.*203T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 426,978 control chromosomes in the GnomAD database, including 38,972 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 0.46 (18470 hom., cov: 31)
  • Exomes 𝑓: 0.36 (20502 hom.)
• Consequence: TRUB1 NM_139169.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRUB1	NM_139169.5	c.*203T>C		3_prime_UTR_variant	8/8	ENST00000298746.5	NP_631908.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRUB1	ENST00000298746.5	c.*203T>C		3_prime_UTR_variant	8/8	1	NM_139169.5	ENSP00000298746	P1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69287 AN: 151774 Hom.: 18431 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.364 AC: 100051 AN: 275086 Hom.: 20502 Cov.: 4 AF XY: 0.364 AC XY: 51349 AN XY: 141000

Gnomad4 AFR exome AF: 0.727

Gnomad4 AMR exome AF: 0.272

Gnomad4 ASJ exome AF: 0.432

Gnomad4 EAS exome AF: 0.0303

Gnomad4 SAS exome AF: 0.390

Gnomad4 FIN exome AF: 0.337

Gnomad4 NFE exome AF: 0.392

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.457 AC: 69380 AN: 151892 Hom.: 18470 Cov.: 31 AF XY: 0.446 AC XY: 33074 AN XY: 74214

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.441

Alfa AF: 0.401 Hom.: 11554

Bravo AF: 0.466

Asia WGS AF: 0.270 AC: 939 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs7071789; hg19: chr10-116735341;