rs16861476

chr3-114065036-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024638.4(QTRT2):c.-21-201T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 152,288 control chromosomes in the GnomAD database, including 482 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 0.076 (482 hom., cov: 32)
• Consequence: QTRT2 NM_024638.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

Genes affected

QTRT2 (HGNC:25771): (queuine tRNA-ribosyltransferase accessory subunit 2) This gene encodes a subunit of tRNA-guanine transglycosylase. tRNA-guanine transglycosylase is a heterodimeric enzyme complex that plays a critical role in tRNA modification by synthesizing the 7-deazaguanosine queuosine, which is found in tRNAs that code for asparagine, aspartic acid, histidine, and tyrosine. The encoded protein may play a role in the queuosine 5'-monophosphate salvage pathway. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QTRT2	NM_024638.4	c.-21-201T>G		intron_variant		ENST00000281273.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QTRT2	ENST00000281273.8	c.-21-201T>G		intron_variant		1	NM_024638.4	P1

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11535 AN: 152168 Hom.: 481 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0915

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0758 AC: 11538 AN: 152288 Hom.: 482 Cov.: 32 AF XY: 0.0751 AC XY: 5588 AN XY: 74452

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0620

Gnomad4 ASJ AF: 0.0915

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0841 Hom.: 576

Bravo AF: 0.0764

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.8
Dann	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs16861476; hg19: chr3-113783883;