rs13314266

Positions:

• chr3-114078270-A-G
• chr3-114078270-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000281273.8(QTRT2):​c.746+1328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,232 control chromosomes in the GnomAD database, including 394 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 0.068 (394 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: QTRT2 ENST00000281273.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.48

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
QTRT2	NM_024638.4	c.746+1328A>G		intron_variant		ENST00000281273.8	NP_078914.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QTRT2	ENST00000281273.8	c.746+1328A>G		intron_variant		1	NM_024638.4	ENSP00000281273	P1

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10371 AN: 152114 Hom.: 394 Cov.: 31

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0546

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0722

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0681 AC: 10372 AN: 152232 Hom.: 394 Cov.: 31 AF XY: 0.0676 AC XY: 5035 AN XY: 74432

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.0539

Gnomad4 ASJ AF: 0.0546

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.0351

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0787

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0756 Hom.: 435

Bravo AF: 0.0683

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	22
DANN	Benign	0.89

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: rs13314266; hg19: chr3-113797117;