chr19-10707416-G-A

Variant names:

• chr19-10707416-G-A
• rs892085
• NM_031209.3:c.530+36G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.59 (26535 hom., cov: 32)
  • Exomes 𝑓: 0.56 (230394 hom.)
• Consequence: QTRT1 NM_031209.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 44 publications found

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]

ACMG classification

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

Selected	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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTRT1	ENST00000250237.10	TSL:1 MANE Select	c.530+36G>A		intron	N/A	ENSP00000250237.4
	QTRT1	ENST00000592254.1	TSL:3	c.473+36G>A		intron	N/A	ENSP00000468811.1
	QTRT1	ENST00000591643.1	TSL:5	c.74+36G>A		intron	N/A	ENSP00000467394.1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89144 AN: 151832 Hom.: 26527 Cov.: 32

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

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.: 32 AF XY: 0.560 AC XY: 406767 AN XY: 726128

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

GnomAD4 genome AF: 0.587 AC: 89184 AN: 151950 Hom.: 26535 Cov.: 32 AF XY: 0.587 AC XY: 43579 AN XY: 74258

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

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
DANN	Benign	0.54
PhyloP100		-0.15
PromoterAI		-0.019	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs892085; hg19: chr19-10818092; COSMIC: COSV51551574; COSMIC: COSV51551574;