rs6935937

Variant names:

• chr6-126170164-T-C
• rs6935937
• ENST00000648977.1:n.*1824-4661T>C

Variant summary

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

The ENST00000648977.1(TRMT11):​n.*1824-4661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,926 control chromosomes in the GnomAD database, including 8,927 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 0.33 (8927 hom., cov: 32)
• Consequence: TRMT11 ENST00000648977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648977.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT11	ENST00000648977.1		n.*1824-4661T>C		intron	N/A	ENSP00000496820.1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50254 AN: 151808 Hom.: 8905 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.331 AC: 50324 AN: 151926 Hom.: 8927 Cov.: 32 AF XY: 0.323 AC XY: 23990 AN XY: 74254

African (AFR) AF: 0.441 AC: 18257 AN: 41434

American (AMR) AF: 0.251 AC: 3827 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5174

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2865 AN: 10476

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22151 AN: 67966

Other (OTH) AF: 0.313 AC: 660 AN: 2106

Alfa AF: 0.320 Hom.: 14195

Bravo AF: 0.331

Asia WGS AF: 0.209 AC: 723 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6935937; hg19: chr6-126491310;