rs3127657

Positions:

• chr6-106656499-T-C
• chr6-106656499-T-G

Variant summary

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

The NM_018292.5(QRSL1):​c.1160+767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,010 control chromosomes in the GnomAD database, including 24,076 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 0.56 (24076 hom., cov: 33)
• Consequence: QRSL1 NM_018292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

QRSL1 (HGNC:21020): (glutaminyl-tRNA amidotransferase subunit QRSL1) Enables glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity. Involved in glutaminyl-tRNAGln biosynthesis via transamidation and mitochondrial translation. Located in mitochondrion. Part of glutamyl-tRNA(Gln) amidotransferase complex. Implicated in combined oxidative phosphorylation deficiency 40. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QRSL1	NM_018292.5	c.1160+767T>C		intron_variant		ENST00000369046.8
QRSL1	XM_011535924.3	c.887+767T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QRSL1	ENST00000369046.8	c.1160+767T>C		intron_variant		1	NM_018292.5	P1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84904 AN: 151892 Hom.: 24042 Cov.: 33

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.539

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.559 AC: 84983 AN: 152010 Hom.: 24076 Cov.: 33 AF XY: 0.557 AC XY: 41410 AN XY: 74292

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.544

Alfa AF: 0.563 Hom.: 8887

Bravo AF: 0.557

Asia WGS AF: 0.465 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.45

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: rs3127657; hg19: chr6-107104374;