6-126041008-T-C

Variant names:

• chr6-126041008-T-C
• rs6900796
• ENST00000648977.1:n.*1369+163T>C

Variant summary

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

The ENST00000648977.1(TRMT11):​n.*1369+163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,924 control chromosomes in the GnomAD database, including 27,707 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 (27707 hom., cov: 32)
• Consequence: TRMT11 ENST00000648977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 10 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]

ENSG00000307282 (HGNC:):

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 = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT11	NR_146797.2	n.1933+2083T>C		intron_variant	Intron 14 of 14
TRMT11	NR_146799.2	n.1492+2083T>C		intron_variant	Intron 13 of 13
TRMT11	NR_146803.2	n.1960+163T>C		intron_variant	Intron 15 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT11	ENST00000648977.1	n.*1369+163T>C		intron_variant	Intron 16 of 22			ENSP00000496820.1
ENSG00000307282	ENST00000824925.1	n.143+952A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88676 AN: 151806 Hom.: 27648 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.585 AC: 88801 AN: 151924 Hom.: 27707 Cov.: 32 AF XY: 0.593 AC XY: 44044 AN XY: 74234

African (AFR) AF: 0.753 AC: 31220 AN: 41448

American (AMR) AF: 0.638 AC: 9738 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3466

East Asian (EAS) AF: 0.944 AC: 4883 AN: 5170

South Asian (SAS) AF: 0.646 AC: 3114 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6136 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30696 AN: 67904

Other (OTH) AF: 0.553 AC: 1165 AN: 2106

Alfa AF: 0.501 Hom.: 75300

Bravo AF: 0.598

Asia WGS AF: 0.774 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.80
PhyloP100		-0.033

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6900796; hg19: chr6-126362154;