dbSNP rs892085: QTRT1:c.530+36G>A (chr19-10707416-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031209.3(QTRT1):c.530+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,611,248 control chromosomes in the GnomAD database, including 256,929 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.59 ( 26535 hom., cov: 32)

Exomes 𝑓: 0.56 ( 230394 hom. )

Consequence

QTRT1
NM_031209.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.153

Publications

44 publications found

Variant links:

Genes affected

QTRT1 (HGNC:23797): (queuine tRNA-ribosyltransferase catalytic subunit 1) This gene encodes the catalytic 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. A pseudogene of this gene is located on the long arm of chromosome X. [provided by RefSeq, Feb 2012]

QTRT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031209.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTRT1	NM_031209.3	MANE Select	c.530+36G>A		intron	N/A	NP_112486.1	Q9BXR0-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
QTRT1	ENST00000250237.10	TSL:1 MANE Select	c.530+36G>A	intron	N/A	ENSP00000250237.4	Q9BXR0-1
QTRT1	ENST00000931299.1		c.530+36G>A	intron	N/A	ENSP00000601358.1
QTRT1	ENST00000931297.1		c.578+36G>A	intron	N/A	ENSP00000601356.1

Frequencies

GnomAD3 genomes

AF:

0.587

AC:

89144

AN:

151832

Hom.:

26527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.541

Gnomad AMR

AF:

0.595

Gnomad ASJ

AF:

0.570

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.627

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.562

GnomAD2 exomes

AF:

0.568

AC:

142450

AN:

250786

AF XY:

0.567

show subpopulations

Gnomad AFR exome

AF:

0.656

Gnomad AMR exome

AF:

0.629

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.332

Gnomad FIN exome

AF:

0.561

Gnomad NFE exome

AF:

0.564

Gnomad OTH exome

AF:

0.546

GnomAD4 exome

AF:

0.559

AC:

816138

AN:

1459298

Hom.:

230394

Cov.:

AF XY:

0.560

AC XY:

406767

AN XY:

726128

show subpopulations

African (AFR)

AF:

0.642

AC:

21465

AN:

33412

American (AMR)

AF:

0.626

AC:

27987

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

14526

AN:

26118

East Asian (EAS)

AF:

0.297

AC:

11769

AN:

39680

South Asian (SAS)

AF:

0.621

AC:

53508

AN:

86216

European-Finnish (FIN)

AF:

0.560

AC:

29908

AN:

53400

Middle Eastern (MID)

AF:

0.468

AC:

2695

AN:

5758

European-Non Finnish (NFE)

AF:

0.560

AC:

621162

AN:

1109708

Other (OTH)

AF:

0.549

AC:

33118

AN:

60294

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

19148

38295

57443

76590

95738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17358

34716

52074

69432

86790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.587

AC:

89184

AN:

151950

Hom.:

26535

Cov.:

AF XY:

0.587

AC XY:

43579

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.652

AC:

27000

AN:

41430

American (AMR)

AF:

0.595

AC:

9076

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.570

AC:

1979

AN:

3470

East Asian (EAS)

AF:

0.324

AC:

1675

AN:

5170

South Asian (SAS)

AF:

0.628

AC:

3026

AN:

4818

European-Finnish (FIN)

AF:

0.553

AC:

5840

AN:

10552

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.571

AC:

38798

AN:

67952

Other (OTH)

AF:

0.559

AC:

1172

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1881

3761

5642

7522

9403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.567

Hom.:

99949

Bravo

AF:

0.585

Asia WGS

AF:

0.520

AC:

1810

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.8

(source)

DANN

Benign

0.54

PhyloP100

-0.15

PromoterAI

-0.019

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over