Variant 12-120522254-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_032314.4(COQ5):c.312G>A(p.Pro104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 1,613,872 control chromosomes in the GnomAD database, including 5,544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.081 ( 562 hom., cov: 33)

Exomes 𝑓: 0.081 ( 4982 hom. )

Consequence

COQ5
NM_032314.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.10

Variant links:

Genes affected

COQ5 (HGNC:28722): (coenzyme Q5, methyltransferase) Enables 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity. Involved in methylation and ubiquinone biosynthetic process. Located in mitochondrial matrix. Part of protein-containing complex. Colocalizes with mitochondrial inner membrane. Implicated in primary coenzyme Q10 deficiency 9. [provided by Alliance of Genome Resources, Apr 2022]

COQ5 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=-0.77).

BP6

Variant 12-120522254-C-T is Benign according to our data. Variant chr12-120522254-C-T is described in ClinVar as [Benign]. Clinvar id is 3060152.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COQ5	NM_032314.4 linkuse as main transcript	c.312G>A	p.Pro104=	synonymous_variant	2/7	ENST00000288532.11	NP_115690.3
COQ5	XM_006719639.3 linkuse as main transcript	c.69G>A	p.Pro23=	synonymous_variant	3/8		XP_006719702.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COQ5	ENST00000288532.11 linkuse as main transcript	c.312G>A	p.Pro104=	synonymous_variant	2/7	1	NM_032314.4	ENSP00000288532	P1

Frequencies

GnomAD3 genomes

AF:

0.0806

AC:

12256

AN:

152026

Hom.:

562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0896

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.0526

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.0372

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0747

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0800

Gnomad OTH

AF:

0.0867

GnomAD3 exomes

AF:

0.0772

AC:

19414

AN:

251414

Hom.:

817

AF XY:

0.0793

AC XY:

10778

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.0907

Gnomad AMR exome

AF:

0.0364

Gnomad ASJ exome

AF:

0.126

Gnomad EAS exome

AF:

0.0408

Gnomad SAS exome

AF:

0.0959

Gnomad FIN exome

AF:

0.0757

Gnomad NFE exome

AF:

0.0846

Gnomad OTH exome

AF:

0.0771

GnomAD4 exome

AF:

0.0806

AC:

117748

AN:

1461726

Hom.:

4982

Cov.:

AF XY:

0.0815

AC XY:

59244

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.0887

Gnomad4 AMR exome

AF:

0.0380

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.0377

Gnomad4 SAS exome

AF:

0.0972

Gnomad4 FIN exome

AF:

0.0822

Gnomad4 NFE exome

AF:

0.0810

Gnomad4 OTH exome

AF:

0.0816

GnomAD4 genome

AF:

0.0806

AC:

12256

AN:

152146

Hom.:

562

Cov.:

AF XY:

0.0801

AC XY:

5956

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0894

Gnomad4 AMR

AF:

0.0525

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.0371

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.0747

Gnomad4 NFE

AF:

0.0800

Gnomad4 OTH

AF:

0.0857

Alfa

AF:

0.0832

Hom.:

929

Bravo

AF:

0.0797

Asia WGS

AF:

0.0670

AC:

234

AN:

3478

EpiCase

AF:

0.0828

EpiControl

AF:

0.0833

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

COQ5-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 23, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.22

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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