16-19073976-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016138.5(COQ7):c.308C>T(p.Thr103Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,612,212 control chromosomes in the GnomAD database, including 325,810 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 25220 hom., cov: 29)

Exomes 𝑓: 0.64 ( 300590 hom. )

Consequence

COQ7
NM_016138.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.17

Variant links:

Genes affected

COQ7 (HGNC:2244): (coenzyme Q7, hydroxylase) The protein encoded by this gene is similar to a mitochondrial di-iron containing hydroxylase in Saccharomyces cerevisiae that is involved with ubiquinone biosynthesis. Mutations in the yeast gene lead to slower development and longer life span. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2010]

COQ7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.3575713E-6).

BP6

Variant 16-19073976-C-T is Benign according to our data. Variant chr16-19073976-C-T is described in ClinVar as [Benign]. Clinvar id is 678528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COQ7	NM_016138.5 link	c.308C>T	p.Thr103Met	missense_variant	Exon 3 of 6	ENST00000321998.10	NP_057222.2	Q99807-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COQ7	ENST00000321998.10 link	c.308C>T	p.Thr103Met	missense_variant	Exon 3 of 6	1	NM_016138.5	ENSP00000322316.5		Q99807-1

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84366

AN:

151308

Hom.:

25201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.617

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.614

GnomAD3 exomes

AF:

0.632

AC:

158578

AN:

250746

Hom.:

51500

AF XY:

0.639

AC XY:

86588

AN XY:

135528

show subpopulations

Gnomad AFR exome

AF:

0.315

Gnomad AMR exome

AF:

0.637

Gnomad ASJ exome

AF:

0.551

Gnomad EAS exome

AF:

0.817

Gnomad SAS exome

AF:

0.653

Gnomad FIN exome

AF:

0.681

Gnomad NFE exome

AF:

0.639

Gnomad OTH exome

AF:

0.636

GnomAD4 exome

AF:

0.638

AC:

931519

AN:

1460786

Hom.:

300590

Cov.:

AF XY:

0.639

AC XY:

464678

AN XY:

726694

show subpopulations

Gnomad4 AFR exome

AF:

0.319

Gnomad4 AMR exome

AF:

0.638

Gnomad4 ASJ exome

AF:

0.546

Gnomad4 EAS exome

AF:

0.826

Gnomad4 SAS exome

AF:

0.651

Gnomad4 FIN exome

AF:

0.677

Gnomad4 NFE exome

AF:

0.640

Gnomad4 OTH exome

AF:

0.630

GnomAD4 genome

AF:

0.558

AC:

84424

AN:

151426

Hom.:

25220

Cov.:

AF XY:

0.566

AC XY:

41824

AN XY:

73938

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.616

Gnomad4 ASJ

AF:

0.530

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.662

Gnomad4 FIN

AF:

0.680

Gnomad4 NFE

AF:

0.636

Gnomad4 OTH

AF:

0.615

Alfa

AF:

0.629

Hom.:

80054

Bravo

AF:

0.545

TwinsUK

AF:

0.641

AC:

2376

ALSPAC

AF:

0.627

AC:

2418

ESP6500AA

AF:

0.339

AC:

1489

ESP6500EA

AF:

0.639

AC:

5496

ExAC

AF:

0.625

AC:

75852

Asia WGS

AF:

0.742

AC:

2576

AN:

3478

EpiCase

AF:

0.650

EpiControl

AF:

0.655

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Primary coenzyme Q10 deficiency 8

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

T;T;T;.;T;.

Eigen

Uncertain

0.25

Eigen_PC

Uncertain

0.24

FATHMM_MKL

Benign

0.29

LIST_S2

Benign

0.74

.;T;T;T;T;T

MetaRNN

Benign

0.0000014

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

L;L;.;.;.;.

PrimateAI

Benign

0.28

PROVEAN

Benign

-1.0

N;N;N;N;N;N

REVEL

Benign

0.083

Sift

Benign

0.058

T;T;T;T;T;T

Sift4G

Uncertain

0.047

D;D;D;D;D;D

Polyphen

0.89

P;P;.;.;.;.

Vest4

0.12

MPC

0.24

ClinPred

0.029

GERP RS

5.9

Varity_R

0.064

gMVP

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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