dbSNP rs13314266: QTRT2:c.746+1328A>G (chr3-114078270-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_024638.4(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
NM_024638.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.48

Publications

3 publications found

Variant links:

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]

QTRT2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_024638.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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: NM_024638.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
QTRT2	NM_024638.4	MANE Select	c.746+1328A>G	intron	N/A	NP_078914.1	Q9H974-1
QTRT2	NM_001256835.2		c.782+1328A>G	intron	N/A	NP_001243764.1	Q9H974-4
QTRT2	NM_001256836.2		c.428+1328A>G	intron	N/A	NP_001243765.1	Q9H974-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
QTRT2	ENST00000281273.8	TSL:1 MANE Select	c.746+1328A>G	intron	N/A	ENSP00000281273.4	Q9H974-1
QTRT2	ENST00000485050.5	TSL:1	c.782+1328A>G	intron	N/A	ENSP00000420682.1	Q9H974-4
QTRT2	ENST00000467703.1	TSL:1	n.1780A>G	non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0682

AC:

10371

AN:

152114

Hom.:

394

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0681

AC:

10372

AN:

152232

Hom.:

394

Cov.:

AF XY:

0.0676

AC XY:

5035

AN XY:

74432

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0787

AC:

5354

AN:

68006

Other (OTH)

AF:

0.0715

AC:

151

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

504

1009

1513

2018

2522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

122

244

366

488

610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.89

PhyloP100

3.5

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over