6-126010399-C-T

Variant summary

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

The NM_001031712.3(TRMT11):c.761-854C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,790 control chromosomes in the GnomAD database, including 27,557 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 0.58 (27557 hom., cov: 31)
• Consequence: TRMT11 NM_001031712.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

Genes affected

TRMT11 (HGNC:21080): (tRNA methyltransferase 11 homolog) Predicted to enable tRNA (guanine-N2-)-methyltransferase activity. Predicted to be involved in tRNA methylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT11	NM_001031712.3	c.761-854C>T		intron_variant		ENST00000334379.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT11	ENST00000334379.11	c.761-854C>T		intron_variant		1	NM_001031712.3	P4

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88657 AN: 151672 Hom.: 27546 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.584 AC: 88699 AN: 151790 Hom.: 27557 Cov.: 31 AF XY: 0.594 AC XY: 44032 AN XY: 74182

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.605

Alfa AF: 0.634 Hom.: 34563

Bravo AF: 0.579

Asia WGS AF: 0.816 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.4
Dann	Benign	0.61

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: rs10485179; hg19: chr6-126331545;