Variant chr6-106629675-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018292.5(QRSL1):c.-7G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,604,704 control chromosomes in the GnomAD database, including 2,851 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.076 ( 1126 hom., cov: 32)

Exomes 𝑓: 0.015 ( 1725 hom. )

Consequence

QRSL1
NM_018292.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

Variant links:

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]

QRSL1 links:

RTN4IP1 (HGNC:):

RTN4IP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 6-106629675-G-A is Benign according to our data. Variant chr6-106629675-G-A is described in ClinVar as [Benign]. Clinvar id is 1270339.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
QRSL1	NM_018292.5 linkuse as main transcript	c.-7G>A	5_prime_UTR_variant	1/11	ENST00000369046.8
QRSL1	XM_011535924.3 linkuse as main transcript	c.-386G>A	5_prime_UTR_variant	1/12
RTN4IP1	NM_001318746.1 linkuse as main transcript	c.-27+652C>T	intron_variant
RTN4IP1	XM_011536192.3 linkuse as main transcript	c.34+168C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QRSL1	ENST00000369046.8 linkuse as main transcript	c.-7G>A	5_prime_UTR_variant	1/11	1	NM_018292.5	P1	Q9H0R6-1
QRSL1	ENST00000369044.1 linkuse as main transcript	c.-7G>A	5_prime_UTR_variant	1/7	2
QRSL1	ENST00000467262.1 linkuse as main transcript	n.77G>A	non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes

AF:

0.0758

AC:

11517

AN:

152008

Hom.:

1114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0882

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.00810

Gnomad FIN

AF:

0.0192

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00197

Gnomad OTH

AF:

0.0545

GnomAD3 exomes

AF:

0.0427

AC:

9867

AN:

230982

Hom.:

778

AF XY:

0.0350

AC XY:

4384

AN XY:

125354

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.0849

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.00550

Gnomad FIN exome

AF:

0.0173

Gnomad NFE exome

AF:

0.00163

Gnomad OTH exome

AF:

0.0244

GnomAD4 exome

AF:

0.0155

AC:

22449

AN:

1452578

Hom.:

1725

Cov.:

AF XY:

0.0142

AC XY:

10240

AN XY:

721612

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.0876

Gnomad4 ASJ exome

AF:

0.00995

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.00672

Gnomad4 FIN exome

AF:

0.0170

Gnomad4 NFE exome

AF:

0.000757

Gnomad4 OTH exome

AF:

0.0294

GnomAD4 genome

AF:

0.0760

AC:

11563

AN:

152126

Hom.:

1126

Cov.:

AF XY:

0.0770

AC XY:

5726

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.0883

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.190

Gnomad4 SAS

AF:

0.00811

Gnomad4 FIN

AF:

0.0192

Gnomad4 NFE

AF:

0.00197

Gnomad4 OTH

AF:

0.0540

Alfa

AF:

0.0176

Hom.:

118

Bravo

AF:

0.0874

Asia WGS

AF:

0.0770

AC:

265

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.0

DANN

Benign

0.85

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over