Genetic Variant NM_016138.5:c.51G>A (chr16-19067715-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_016138.5(COQ7):c.51G>A(p.Pro17Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,606,028 control chromosomes in the GnomAD database, including 27,606 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2518 hom., cov: 33)

Exomes 𝑓: 0.18 ( 25088 hom. )

Consequence

COQ7
NM_016138.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.727

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:

COQ7-DT (HGNC:55362): (COQ7 divergent transcript)

COQ7-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 16-19067715-G-A is Benign according to our data. Variant chr16-19067715-G-A is described in ClinVar as [Benign]. Clinvar id is 669700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.727 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COQ7	NM_016138.5 link	c.51G>A	p.Pro17Pro	synonymous_variant	Exon 1 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.51G>A	p.Pro17Pro	synonymous_variant	Exon 1 of 6	1	NM_016138.5	ENSP00000322316.5		Q99807-1

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27136

AN:

152088

Hom.:

2519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.0869

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.178

GnomAD3 exomes

AF:

0.180

AC:

42008

AN:

233386

Hom.:

3956

AF XY:

0.173

AC XY:

22238

AN XY:

128448

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.233

Gnomad ASJ exome

AF:

0.179

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.0946

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.191

Gnomad OTH exome

AF:

0.185

GnomAD4 exome

AF:

0.182

AC:

264167

AN:

1453822

Hom.:

25088

Cov.:

AF XY:

0.179

AC XY:

129420

AN XY:

723454

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.229

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.148

Gnomad4 SAS exome

AF:

0.0947

Gnomad4 FIN exome

AF:

0.212

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.178

AC:

27137

AN:

152206

Hom.:

2518

Cov.:

AF XY:

0.179

AC XY:

13293

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.0857

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.193

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.192

Hom.:

973

Bravo

AF:

0.179

Asia WGS

AF:

0.0990

AC:

343

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

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. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

4.6

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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