3-114078270-A-G

Variant names:

• chr3-114078270-A-G
• rs13314266
• ENST00000467703.1:n.1780A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000467703.1(QTRT2):​n.1780A>G variant causes a non coding transcript exon 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 ENST00000467703.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.48
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTRT2	NM_024638.4	MANE Select	c.746+1328A>G		intron	N/A	NP_078914.1
	QTRT2	NM_001256835.2		c.782+1328A>G		intron	N/A	NP_001243764.1
	QTRT2	NM_001256836.2		c.428+1328A>G		intron	N/A	NP_001243765.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTRT2	ENST00000467703.1	TSL:1	n.1780A>G		non_coding_transcript_exon	Exon 3 of 3
	QTRT2	ENST00000281273.8	TSL:1 MANE Select	c.746+1328A>G		intron	N/A	ENSP00000281273.4
	QTRT2	ENST00000485050.5	TSL:1	c.782+1328A>G		intron	N/A	ENSP00000420682.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0624 AC: 2591 AN: 41544

American (AMR) AF: 0.0539 AC: 824 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0546 AC: 189 AN: 3464

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.0351 AC: 169 AN: 4818

European-Finnish (FIN) AF: 0.0649 AC: 688 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5354 AN: 68006

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0747 Hom.: 550

Bravo AF: 0.0683

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	22
DANN	Benign	0.89
PhyloP100		3.5
Mutation Taster		=96/4	polymorphism (auto)

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: rs13314266; hg19: chr3-113797117;