rs6117011

Variant names:

• chr20-5942184-C-T
• rs6117011
• NM_015939.5:c.1027-148G>A

Variant summary

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

The NM_015939.5(TRMT6):​c.1027-148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 772,334 control chromosomes in the GnomAD database, including 2,292 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 0.067 (657 hom., cov: 32)
  • Exomes 𝑓: 0.044 (1635 hom.)
• Consequence: TRMT6 NM_015939.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 0 publications found

Genes affected

TRMT6 (HGNC:20900): (tRNA methyltransferase 6 non-catalytic subunit) This gene encodes a member of the tRNA methyltransferase 6 protein family. A similar protein in yeast is part of a two component methyltransferase, which is involved in the posttranslational modification that produces the modified nucleoside 1-methyladenosine in tRNAs. Modified 1-methyladenosine influences initiator methionine stability and may be involved in the replication of human immunodeficiency virus type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015939.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT6	NM_015939.5	MANE Select	c.1027-148G>A		intron	N/A	NP_057023.2
	TRMT6	NM_001281467.2		c.517-148G>A		intron	N/A	NP_001268396.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT6	ENST00000203001.7	TSL:1 MANE Select	c.1027-148G>A		intron	N/A	ENSP00000203001.2
	TRMT6	ENST00000453074.6	TSL:2	c.517-148G>A		intron	N/A	ENSP00000392070.2
	TRMT6	ENST00000466974.5	TSL:2	n.1099-148G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0675 AC: 10264 AN: 152108 Hom.: 656 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.00783

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0598

GnomAD4 exome AF: 0.0437 AC: 27068 AN: 620108 Hom.: 1635 AF XY: 0.0443 AC XY: 14555 AN XY: 328308

African (AFR) AF: 0.145 AC: 2277 AN: 15676

American (AMR) AF: 0.0977 AC: 2462 AN: 25210

Ashkenazi Jewish (ASJ) AF: 0.0293 AC: 486 AN: 16594

East Asian (EAS) AF: 0.236 AC: 7967 AN: 33806

South Asian (SAS) AF: 0.0779 AC: 4223 AN: 54202

European-Finnish (FIN) AF: 0.0101 AC: 350 AN: 34530

Middle Eastern (MID) AF: 0.0323 AC: 76 AN: 2350

European-Non Finnish (NFE) AF: 0.0192 AC: 7772 AN: 405540

Other (OTH) AF: 0.0452 AC: 1455 AN: 32200

GnomAD4 genome AF: 0.0675 AC: 10272 AN: 152226 Hom.: 657 Cov.: 32 AF XY: 0.0669 AC XY: 4977 AN XY: 74426

African (AFR) AF: 0.141 AC: 5842 AN: 41532

American (AMR) AF: 0.0748 AC: 1144 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1216 AN: 5170

South Asian (SAS) AF: 0.0846 AC: 408 AN: 4822

European-Finnish (FIN) AF: 0.00783 AC: 83 AN: 10596

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0194 AC: 1318 AN: 68022

Other (OTH) AF: 0.0605 AC: 128 AN: 2114

Alfa AF: 0.0488 Hom.: 60

Bravo AF: 0.0781

Asia WGS AF: 0.131 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-1.4
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: rs6117011; hg19: chr20-5922830;