rs3732788

Variant names:

• chr3-114086012-T-C
• rs3732788
• NM_024638.4:c.*108T>C

Variant summary

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

The NM_001256835.2(QTRT2):​c.*108T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 892,434 control chromosomes in the GnomAD database, including 4,168 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 0.10 (893 hom., cov: 32)
  • Exomes 𝑓: 0.090 (3275 hom.)
• Consequence: QTRT2 NM_001256835.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 6 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256835.2. 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
	QTRT2	NM_024638.4	MANE Select	c.*108T>C		3_prime_UTR	Exon 10 of 10	NP_078914.1
	QTRT2	NM_001256835.2		c.*108T>C		3_prime_UTR	Exon 9 of 9	NP_001243764.1
	QTRT2	NM_001256836.2		c.*108T>C		3_prime_UTR	Exon 6 of 6	NP_001243765.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTRT2	ENST00000281273.8	TSL:1 MANE Select	c.*108T>C		3_prime_UTR	Exon 10 of 10	ENSP00000281273.4
	QTRT2	ENST00000485050.5	TSL:1	c.*108T>C		3_prime_UTR	Exon 9 of 9	ENSP00000420682.1
	QTRT2	ENST00000929110.1		c.*108T>C		3_prime_UTR	Exon 10 of 10	ENSP00000599169.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15415 AN: 152136 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0903 AC: 66860 AN: 740180 Hom.: 3275 Cov.: 10 AF XY: 0.0902 AC XY: 34729 AN XY: 384852

African (AFR) AF: 0.155 AC: 2797 AN: 18034

American (AMR) AF: 0.0498 AC: 1594 AN: 31976

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 1854 AN: 18236

East Asian (EAS) AF: 0.125 AC: 4158 AN: 33234

South Asian (SAS) AF: 0.0904 AC: 5413 AN: 59858

European-Finnish (FIN) AF: 0.0477 AC: 1872 AN: 39276

Middle Eastern (MID) AF: 0.103 AC: 407 AN: 3960

European-Non Finnish (NFE) AF: 0.0905 AC: 45229 AN: 499546

Other (OTH) AF: 0.0981 AC: 3536 AN: 36060

GnomAD4 genome AF: 0.101 AC: 15444 AN: 152254 Hom.: 893 Cov.: 32 AF XY: 0.0994 AC XY: 7397 AN XY: 74452

African (AFR) AF: 0.145 AC: 6021 AN: 41548

American (AMR) AF: 0.0715 AC: 1094 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.134 AC: 695 AN: 5180

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4822

European-Finnish (FIN) AF: 0.0495 AC: 525 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5987 AN: 68010

Other (OTH) AF: 0.113 AC: 240 AN: 2116

Alfa AF: 0.0927 Hom.: 886

Bravo AF: 0.107

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.23
PhyloP100		-0.54
Mutation Taster		=100/0	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: rs3732788; hg19: chr3-113804859;