chr6-126062330-G-A

Variant names:

• chr6-126062330-G-A
• rs1569741
• XR_007059300.1:n.4255G>A

Variant summary

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

The XR_007059300.1(TRMT11):​n.4255G>A 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 0.57 in 152,126 control chromosomes in the GnomAD database, including 26,385 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 0.57 (26385 hom., cov: 33)
• Consequence: TRMT11 XR_007059300.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT11	XR_007059300.1	n.4255G>A		non_coding_transcript_exon_variant	Exon 15 of 16
TRMT11	XR_007059315.1	n.4204G>A		non_coding_transcript_exon_variant	Exon 14 of 15
TRMT11	XR_007059316.1	n.4388G>A		non_coding_transcript_exon_variant	Exon 17 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT11	ENST00000648977.1	n.*1437+9140G>A		intron_variant	Intron 17 of 22			ENSP00000496820.1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86528 AN: 152008 Hom.: 26329 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.570 AC: 86650 AN: 152126 Hom.: 26385 Cov.: 33 AF XY: 0.578 AC XY: 42968 AN XY: 74368

African (AFR) AF: 0.734 AC: 30483 AN: 41510

American (AMR) AF: 0.635 AC: 9702 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4765 AN: 5184

South Asian (SAS) AF: 0.604 AC: 2915 AN: 4826

European-Finnish (FIN) AF: 0.574 AC: 6067 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29852 AN: 67954

Other (OTH) AF: 0.543 AC: 1150 AN: 2116

Alfa AF: 0.463 Hom.: 9015

Bravo AF: 0.584

Asia WGS AF: 0.742 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.61
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1569741; hg19: chr6-126383476;