rs9375427

Variant names:

• chr6-126168180-G-T
• rs9375427
• ENST00000648977.1:n.*1824-6645G>T

Variant summary

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

The ENST00000648977.1(TRMT11):​n.*1824-6645G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,948 control chromosomes in the GnomAD database, including 3,413 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 0.21 (3413 hom., cov: 32)
• Consequence: TRMT11 ENST00000648977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 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.*1824-6645G>T		intron	N/A	ENSP00000496820.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31625 AN: 151830 Hom.: 3416 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.208 AC: 31639 AN: 151948 Hom.: 3413 Cov.: 32 AF XY: 0.201 AC XY: 14898 AN XY: 74242

African (AFR) AF: 0.211 AC: 8732 AN: 41436

American (AMR) AF: 0.176 AC: 2687 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3468

East Asian (EAS) AF: 0.0747 AC: 386 AN: 5170

South Asian (SAS) AF: 0.0880 AC: 423 AN: 4806

European-Finnish (FIN) AF: 0.161 AC: 1698 AN: 10560

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16106 AN: 67904

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.223 Hom.: 6830

Bravo AF: 0.210

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.37
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9375427; hg19: chr6-126489326; COSMIC: COSV60279800;