6-126010399-C-T

Variant names:

• chr6-126010399-C-T
• rs10485179
• NM_001031712.3:c.761-854C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350590.2(TRMT11):​c.-508C>T variant causes a 5 prime UTR 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_001350590.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350590.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT11	NM_001031712.3	MANE Select	c.761-854C>T		intron	N/A	NP_001026882.2
	TRMT11	NM_001350590.2		c.-508C>T		5_prime_UTR	Exon 10 of 15	NP_001337519.1
	TRMT11	NM_001350593.2		c.-508C>T		5_prime_UTR	Exon 11 of 16	NP_001337522.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT11	ENST00000334379.11	TSL:1 MANE Select	c.761-854C>T		intron	N/A	ENSP00000333934.5
	TRMT11	ENST00000466316.1	TSL:5	n.*181-854C>T		intron	N/A	ENSP00000466001.3
	TRMT11	ENST00000479748.5	TSL:1	n.*176-854C>T		intron	N/A	ENSP00000433724.1

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

African (AFR) AF: 0.368 AC: 15250 AN: 41400

American (AMR) AF: 0.688 AC: 10471 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3468

East Asian (EAS) AF: 0.950 AC: 4915 AN: 5176

South Asian (SAS) AF: 0.751 AC: 3613 AN: 4812

European-Finnish (FIN) AF: 0.710 AC: 7484 AN: 10542

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42743 AN: 67854

Other (OTH) AF: 0.605 AC: 1277 AN: 2112

Alfa AF: 0.626 Hom.: 43009

Bravo AF: 0.579

Asia WGS AF: 0.816 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.61
PhyloP100		0.30
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: rs10485179; hg19: chr6-126331545;