rs952020

Variant names:

• chr6-126114581-G-A
• rs952020
• XR_007059314.1:n.16258G>A

Variant summary

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

The XR_007059314.1(TRMT11):​n.16258G>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 0.21 in 152,022 control chromosomes in the GnomAD database, including 6,905 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 (6905 hom., cov: 32)
• Consequence: TRMT11 XR_007059314.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT11	XR_007059314.1	n.16258G>A		non_coding_transcript_exon_variant	Exon 14 of 15
TRMT11	XR_007059289.1	n.1582-124G>A		intron_variant	Intron 14 of 17
TRMT11	XR_007059290.1	n.1633-124G>A		intron_variant	Intron 15 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT11	ENST00000648977.1	n.*1527-124G>A		intron_variant	Intron 18 of 22			ENSP00000496820.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31875 AN: 151904 Hom.: 6875 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.210 AC: 31963 AN: 152022 Hom.: 6905 Cov.: 32 AF XY: 0.205 AC XY: 15221 AN XY: 74324

African (AFR) AF: 0.557 AC: 23082 AN: 41448

American (AMR) AF: 0.103 AC: 1568 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 274 AN: 3466

East Asian (EAS) AF: 0.0772 AC: 398 AN: 5154

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4828

European-Finnish (FIN) AF: 0.0719 AC: 763 AN: 10612

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5079 AN: 67940

Other (OTH) AF: 0.188 AC: 396 AN: 2110

Alfa AF: 0.159 Hom.: 538

Bravo AF: 0.226

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.45
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs952020; hg19: chr6-126435727;