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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT10B	XM_011517735.4	c.-223G>A		5_prime_UTR_variant	Exon 1 of 9		XP_011516037.1
TRMT10B	XM_011517736.4	c.-223G>A		5_prime_UTR_variant	Exon 1 of 9		XP_011516038.1
TRMT10B	XM_047422833.1	c.-223G>A		5_prime_UTR_variant	Exon 1 of 9		XP_047278789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255872	ENST00000540557.1	n.*911-25033C>T		intron_variant	Intron 9 of 11	5		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 v4.3

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

Other links and lift over

dbSNP: rs7861041; hg19: chr9-37753058;