rs1268121

chr6-126031440-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001031712.3(TRMT11):c.1261-7265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,102 control chromosomes in the GnomAD database, including 1,680 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 0.14 (1680 hom., cov: 32)
• Consequence: TRMT11 NM_001031712.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT11	NM_001031712.3	c.1261-7265A>G		intron_variant		ENST00000334379.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT11	ENST00000334379.11	c.1261-7265A>G		intron_variant		1	NM_001031712.3	P4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20557 AN: 151984 Hom.: 1681 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.135 AC: 20554 AN: 152102 Hom.: 1680 Cov.: 32 AF XY: 0.132 AC XY: 9840 AN XY: 74360

Gnomad4 AFR AF: 0.0726

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.00330

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.170

Alfa AF: 0.143 Hom.: 647

Bravo AF: 0.135

Asia WGS AF: 0.0780 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.066
Dann	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs1268121; hg19: chr6-126352586;