chr6-106629627-G-A

Position:

• chr6-106629627-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018292.5(QRSL1):​c.-55G>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.38 in 1,569,286 control chromosomes in the GnomAD database, including 118,536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.31 (8349 hom., cov: 32)
  • Exomes 𝑓: 0.39 (110187 hom.)
• Consequence: QRSL1 NM_018292.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.77

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]

RTN4IP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-106629627-G-A is Benign according to our data. Variant chr6-106629627-G-A is described in ClinVar as [Benign]. Clinvar id is 1288288.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QRSL1	NM_018292.5	c.-55G>A		5_prime_UTR_variant	1/11	ENST00000369046.8
QRSL1	XM_011535924.3	c.-434G>A		5_prime_UTR_variant	1/12
RTN4IP1	NM_001318746.1	c.-27+700C>T		intron_variant
RTN4IP1	XM_011536192.3	c.34+216C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QRSL1	ENST00000369046.8	c.-55G>A		5_prime_UTR_variant	1/11	1	NM_018292.5	P1
QRSL1	ENST00000369044.1	c.-55G>A		5_prime_UTR_variant	1/7	2
QRSL1	ENST00000467262.1	n.29G>A		non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46727 AN: 151952 Hom.: 8344 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.388 AC: 550003 AN: 1417216 Hom.: 110187 Cov.: 31 AF XY: 0.388 AC XY: 272208 AN XY: 701168

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.315

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.0731

Gnomad4 SAS exome AF: 0.357

Gnomad4 FIN exome AF: 0.372

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.362

GnomAD4 genome AF: 0.307 AC: 46743 AN: 152070 Hom.: 8349 Cov.: 32 AF XY: 0.304 AC XY: 22602 AN XY: 74328

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.309

Alfa AF: 0.378 Hom.: 6138

Bravo AF: 0.293

Asia WGS AF: 0.223 AC: 774 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	19
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.32		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.32		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs2054365; hg19: chr6-107077502; COSMIC: COSV64687105; COSMIC: COSV64687105;