ENST00000715728.1:c.-300G>T

Variant names:

• chr11-64317826-C-A
• rs9787810
• ENST00000715728.1:c.-300G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000715728.1(TRMT112):​c.-300G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: TRMT112 ENST00000715728.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 23 publications found

Genes affected

TRMT112 (HGNC:26940): (tRNA methyltransferase activator subunit 11-2) Enables protein heterodimerization activity and protein methyltransferase activity. Involved in macromolecule methylation and positive regulation of rRNA processing. Located in nucleoplasm and perinuclear region of cytoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT112	NM_001372071.1	c.-146-154G>T		intron_variant	Intron 1 of 4		NP_001359000.1
TRMT112	NM_001372072.1	c.-147+133G>T		intron_variant	Intron 1 of 4		NP_001359001.1
TRMT112	XM_047427118.1	c.-281-19G>T		intron_variant	Intron 1 of 4		XP_047283074.1
TRMT112	XM_047427119.1	c.-281-19G>T		intron_variant	Intron 1 of 4		XP_047283075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT112	ENST00000715728.1	c.-300G>T		5_prime_UTR_variant	Exon 1 of 4			ENSP00000520509.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 4645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.3
DANN	Benign	0.63
PhyloP100		-1.3
PromoterAI		-0.0051	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.27		Position offset: -3

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

Other links and lift over

dbSNP: rs9787810; hg19: chr11-64085298;