chr6-126031440-A-G

Variant names:

• chr6-126031440-A-G
• rs1268121
• NM_001031712.3:c.1261-7265A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031712.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT11	NM_001031712.3	MANE Select	c.1261-7265A>G		intron	N/A	NP_001026882.2	Q7Z4G4-1
	TRMT11	NM_001350580.2		c.1225-7265A>G		intron	N/A	NP_001337509.1
	TRMT11	NM_001350581.2		c.1072-7265A>G		intron	N/A	NP_001337510.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT11	ENST00000334379.11	TSL:1 MANE Select	c.1261-7265A>G		intron	N/A	ENSP00000333934.5	Q7Z4G4-1
	TRMT11	ENST00000466316.1	TSL:5	n.*667-7265A>G		intron	N/A	ENSP00000466001.3
	TRMT11	ENST00000479748.5	TSL:1	n.*676-7265A>G		intron	N/A	ENSP00000433724.1	Q7Z4G4-3

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

African (AFR) AF: 0.0726 AC: 3014 AN: 41526

American (AMR) AF: 0.113 AC: 1729 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3472

East Asian (EAS) AF: 0.00330 AC: 17 AN: 5154

South Asian (SAS) AF: 0.104 AC: 503 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1342 AN: 10576

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12358 AN: 67968

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.151 Hom.: 1492

Bravo AF: 0.135

Asia WGS AF: 0.0780 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.066
DANN	Benign	0.50
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1268121; hg19: chr6-126352586;