chr9-128332174-G-A

Position:

chr9-128332174-G-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2

The NM_016035.5(COQ4):c.424G>A(p.Ala142Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00548 in 1,582,382 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0037 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 82 hom. )

Consequence

COQ4
NM_016035.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 4.85

Variant links:

Genes affected

COQ4 (HGNC:19693): (coenzyme Q4) This gene encodes a component of the coenzyme Q biosynthesis pathway. Coenzyme Q, an essential component of the electron transport chain, shuttles electrons between complexes I or II to complex III of the mitochondrial transport chain. This protein appears to play a structural role in stabilizing a complex that contains most of the coenzyme Q biosynthesis enzymes. Mutations in this gene are associated with mitochondrial disorders linked to coenzyme Q deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

COQ4 links:

COQ4 (HGNC:):

COQ4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a chain Ubiquinone biosynthesis protein COQ4 homolog, mitochondrial (size 234) in uniprot entity COQ4_HUMAN there are 27 pathogenic changes around while only 3 benign (90%) in NM_016035.5

BP4

Computational evidence support a benign effect (MetaRNN=0.007909).

BP6

Variant 9-128332174-G-A is Benign according to our data. Variant chr9-128332174-G-A is described in ClinVar as [Benign]. Clinvar id is 383917.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0037 (564/152312) while in subpopulation SAS AF= 0.0334 (161/4820). AF 95% confidence interval is 0.0292. There are 5 homozygotes in gnomad4. There are 310 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COQ4	NM_016035.5 linkuse as main transcript	c.424G>A	p.Ala142Thr	missense_variant	5/7	ENST00000300452.8	NP_057119.3	Q9Y3A0-1
COQ4	XM_047423449.1 linkuse as main transcript	c.*24G>A		3_prime_UTR_variant	4/4		XP_047279405.1
COQ4	NM_001305942.2 linkuse as main transcript	c.*3-1300G>A		intron_variant			NP_001292871.2	A0A024R890
COQ4	XM_017014792.2 linkuse as main transcript	c.*3-676G>A		intron_variant			XP_016870281.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COQ4	ENST00000300452.8 linkuse as main transcript	c.424G>A	p.Ala142Thr	missense_variant	5/7	1	NM_016035.5	ENSP00000300452.3		Q9Y3A0-1
COQ4	ENST00000461102.1 linkuse as main transcript	n.1763G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00372

AC:

566

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000772

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0336

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00453

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00691

AC:

1386

AN:

200580

Hom.:

AF XY:

0.00862

AC XY:

929

AN XY:

107720

show subpopulations

Gnomad AFR exome

AF:

0.000904

Gnomad AMR exome

AF:

0.00155

Gnomad ASJ exome

AF:

0.00177

Gnomad EAS exome

AF:

0.000134

Gnomad SAS exome

AF:

0.0331

Gnomad FIN exome

AF:

0.000456

Gnomad NFE exome

AF:

0.00495

Gnomad OTH exome

AF:

0.00388

GnomAD4 exome

AF:

0.00567

AC:

8109

AN:

1430070

Hom.:

Cov.:

AF XY:

0.00657

AC XY:

4655

AN XY:

708620

show subpopulations

Gnomad4 AFR exome

AF:

0.00122

Gnomad4 AMR exome

AF:

0.00164

Gnomad4 ASJ exome

AF:

0.00212

Gnomad4 EAS exome

AF:

0.0000527

Gnomad4 SAS exome

AF:

0.0331

Gnomad4 FIN exome

AF:

0.000371

Gnomad4 NFE exome

AF:

0.00438

Gnomad4 OTH exome

AF:

0.00545

GnomAD4 genome

AF:

0.00370

AC:

564

AN:

152312

Hom.:

Cov.:

AF XY:

0.00416

AC XY:

310

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0334

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00453

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00446

Hom.:

Bravo

AF:

0.00331

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00372

AC:

ExAC

AF:

0.00621

AC:

751

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 23, 2016	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 20, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.55

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.17

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Benign

0.66

LIST_S2

Uncertain

0.91

MetaRNN

Benign

0.0079

MetaSVM

Benign

-0.84

MutationAssessor

Uncertain

2.3

PrimateAI

Benign

0.37

PROVEAN

Benign

-1.3

REVEL

Benign

0.16

Sift

Benign

0.45

Sift4G

Benign

0.51

Polyphen

0.98

Vest4

0.23

MVP

0.59

MPC

0.61

ClinPred

0.033

GERP RS

5.8

Varity_R

0.054

gMVP

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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