rs11197010

chr10-114955200-C-T

Variant summary

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

The NM_139169.5(TRUB1):c.441+4051C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,062 control chromosomes in the GnomAD database, including 22,035 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 0.51 (22035 hom., cov: 32)
• Consequence: TRUB1 NM_139169.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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=-0.95).
• 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	UniProt
TRUB1	NM_139169.5	c.441+4051C>T		intron_variant		ENST00000298746.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRUB1	ENST00000298746.5	c.441+4051C>T		intron_variant		1	NM_139169.5	P1
TRUB1	ENST00000485065.1	n.309+4051C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77586 AN: 151942 Hom.: 21991 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77684 AN: 152062 Hom.: 22035 Cov.: 32 AF XY: 0.502 AC XY: 37290 AN XY: 74322

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.525

Alfa AF: 0.475 Hom.: 3102

Bravo AF: 0.512

Asia WGS AF: 0.289 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.6
Dann	Benign	0.31

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: rs11197010; hg19: chr10-116714959;