rs11963634

Positions:

• chr6-126121237-A-G

Variant summary

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

The XR_007059297.1(TRMT11):​n.7210A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,124 control chromosomes in the GnomAD database, including 4,136 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 0.20 (4136 hom., cov: 33)
• Consequence: TRMT11 XR_007059297.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRMT11	XR_007059297.1	n.7210A>G		non_coding_transcript_exon_variant	18/19
TRMT11	XR_007059314.1	n.22914A>G		non_coding_transcript_exon_variant	14/15
TRMT11	XR_007059289.1	n.1777+5382A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRMT11	ENST00000648977.1	c.*1823+5382A>G		intron_variant, NMD_transcript_variant				ENSP00000496820

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30520 AN: 152006 Hom.: 4136 Cov.: 33

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00522

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.201 AC: 30522 AN: 152124 Hom.: 4136 Cov.: 33 AF XY: 0.195 AC XY: 14507 AN XY: 74372

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.00523

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.218

Alfa AF: 0.262 Hom.: 2101

Bravo AF: 0.189

Asia WGS AF: 0.103 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11963634; hg19: chr6-126442383;