4-83271015-G-C

Variant summary

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

The NM_001358921.2(COQ2):​c.629-1022C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,976 control chromosomes in the GnomAD database, including 29,234 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.62 ( 29234 hom., cov: 31)

Consequence

COQ2
NM_001358921.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0270
Variant links:
Genes affected
COQ2 (HGNC:25223): (coenzyme Q2, polyprenyltransferase) This gene encodes an enzyme that functions in the final steps in the biosynthesis of CoQ (ubiquinone), a redox carrier in the mitochondrial respiratory chain and a lipid-soluble antioxidant. This enzyme, which is part of the coenzyme Q10 pathway, catalyzes the prenylation of parahydroxybenzoate with an all-trans polyprenyl group. Mutations in this gene cause coenzyme Q10 deficiency, a mitochondrial encephalomyopathy, and also COQ2 nephropathy, an inherited form of mitochondriopathy with primary renal involvement. [provided by RefSeq, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 4-83271015-G-C is Benign according to our data. Variant chr4-83271015-G-C is described in ClinVar as [Benign]. Clinvar id is 226000.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COQ2NM_001358921.2 linkc.629-1022C>G intron_variant Intron 4 of 6 ENST00000647002.2 NP_001345850.1
COQ2NM_015697.9 linkc.779-1022C>G intron_variant Intron 4 of 6 NP_056512.5 Q96H96-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COQ2ENST00000647002.2 linkc.629-1022C>G intron_variant Intron 4 of 6 NM_001358921.2 ENSP00000495761.2 Q96H96-1

Frequencies

GnomAD3 genomes
AF:
0.617
AC:
93643
AN:
151858
Hom.:
29223
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.544
Gnomad AMI
AF:
0.619
Gnomad AMR
AF:
0.621
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.851
Gnomad SAS
AF:
0.688
Gnomad FIN
AF:
0.728
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.621
Gnomad OTH
AF:
0.598
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.616
AC:
93683
AN:
151976
Hom.:
29234
Cov.:
31
AF XY:
0.624
AC XY:
46379
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.544
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.595
Gnomad4 EAS
AF:
0.850
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.728
Gnomad4 NFE
AF:
0.621
Gnomad4 OTH
AF:
0.599
Alfa
AF:
0.617
Hom.:
3477
Bravo
AF:
0.606
Asia WGS
AF:
0.764
AC:
2659
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.5
DANN
Benign
0.68

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.

Other links and lift over

dbSNP: rs4693075; hg19: chr4-84192168; API