rs7861041

Variant names:

• chr9-37753061-G-A
• rs7861041
• ENST00000540557.1:n.*911-25033C>T

Variant summary

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

The ENST00000540557.1(ENSG00000255872):​n.*911-25033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,510 control chromosomes in the GnomAD database, including 2,534 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 0.18 (2534 hom., cov: 30)
• Consequence: ENSG00000255872 ENST00000540557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 8 publications found

Genes affected

ENSG00000255872 (HGNC:):

TRMT10B (HGNC:26454): (tRNA methyltransferase 10B) Enables tRNA (guanine-N1-)-methyltransferase activity. Predicted to be involved in mitochondrial tRNA processing. Located in cytosol. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540557.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255872	ENST00000540557.1	TSL:5	n.*911-25033C>T		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27280 AN: 151396 Hom.: 2529 Cov.: 30

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.180 AC: 27303 AN: 151510 Hom.: 2534 Cov.: 30 AF XY: 0.179 AC XY: 13268 AN XY: 73980

African (AFR) AF: 0.182 AC: 7509 AN: 41282

American (AMR) AF: 0.164 AC: 2487 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.0996 AC: 512 AN: 5138

South Asian (SAS) AF: 0.227 AC: 1084 AN: 4778

European-Finnish (FIN) AF: 0.208 AC: 2193 AN: 10530

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12621 AN: 67838

Other (OTH) AF: 0.163 AC: 342 AN: 2096

Alfa AF: 0.177 Hom.: 4123

Bravo AF: 0.175

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		0.17

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7861041;

hg19: chr9-37753058;