16-19078240-C-G

Position:

• chr16-19078240-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_016138.5(COQ7):​c.*82C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,017,492 control chromosomes in the GnomAD database, including 17,818 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.18 (2510 hom., cov: 31)
  • Exomes 𝑓: 0.18 (15308 hom.)
• Consequence: COQ7 NM_016138.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.40

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 16-19078240-C-G is Benign according to our data. Variant chr16-19078240-C-G is described in ClinVar as [Benign]. Clinvar id is 1288927.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COQ7	NM_016138.5	c.*82C>G		3_prime_UTR_variant	6/6	ENST00000321998.10	NP_057222.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COQ7	ENST00000321998.10	c.*82C>G		3_prime_UTR_variant	6/6	1	NM_016138.5	ENSP00000322316	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27055 AN: 150770 Hom.: 2511 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.179

GnomAD4 exome AF: 0.181 AC: 157092 AN: 866648 Hom.: 15308 Cov.: 11 AF XY: 0.178 AC XY: 79227 AN XY: 444728

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.225

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.0943

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.179 AC: 27057 AN: 150844 Hom.: 2510 Cov.: 31 AF XY: 0.180 AC XY: 13240 AN XY: 73618

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.178

Alfa AF: 0.115 Hom.: 226

Bravo AF: 0.179

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.28
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs8051232; hg19: chr16-19089562;