chr3-114086012-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024638.4(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_024638.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QTRT2	NM_024638.4	c.*108T>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000281273.8	NP_078914.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QTRT2	ENST00000281273.8	c.*108T>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_024638.4	ENSP00000281273.4

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

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.0498

Gnomad4 ASJ exome AF: 0.102

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.0904

Gnomad4 FIN exome AF: 0.0477

Gnomad4 NFE exome AF: 0.0905

Gnomad4 OTH exome AF: 0.0981

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0907 Hom.: 652

Bravo AF: 0.107

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.23

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

Publications

LitVar

Other links and lift over

dbSNP: rs3732788; hg19: chr3-113804859;