rs11197010

Variant names:

• chr10-114955200-C-T
• rs11197010
• NM_139169.5:c.441+4051C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRUB1	NM_139169.5	c.441+4051C>T		intron_variant	Intron 3 of 7	ENST00000298746.5	NP_631908.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRUB1	ENST00000298746.5	c.441+4051C>T		intron_variant	Intron 3 of 7	1	NM_139169.5	ENSP00000298746.3
TRUB1	ENST00000485065.1	n.309+4051C>T		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.749 AC: 31077 AN: 41496

American (AMR) AF: 0.366 AC: 5592 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3470

East Asian (EAS) AF: 0.0362 AC: 187 AN: 5170

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4443 AN: 10546

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31038 AN: 67966

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

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
PhyloP100		0.0010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11197010; hg19: chr10-116714959;