16-19078240-C-G

Variant names:

• chr16-19078240-C-G
• rs8051232
• NM_016138.5:c.*82C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
COQ7	NM_016138.5	c.*82C>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000321998.10	NP_057222.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COQ7	ENST00000321998.10	c.*82C>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_016138.5	ENSP00000322316.5

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

African (AFR) AF: 0.142 AC: 2644 AN: 18592

American (AMR) AF: 0.225 AC: 5444 AN: 24156

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 3394 AN: 18460

East Asian (EAS) AF: 0.148 AC: 4724 AN: 31950

South Asian (SAS) AF: 0.0943 AC: 5399 AN: 57262

European-Finnish (FIN) AF: 0.213 AC: 10014 AN: 47012

Middle Eastern (MID) AF: 0.123 AC: 530 AN: 4320

European-Non Finnish (NFE) AF: 0.189 AC: 118093 AN: 625886

Other (OTH) AF: 0.176 AC: 6850 AN: 39010

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

African (AFR) AF: 0.146 AC: 5996 AN: 41178

American (AMR) AF: 0.214 AC: 3244 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3464

East Asian (EAS) AF: 0.148 AC: 763 AN: 5142

South Asian (SAS) AF: 0.0867 AC: 413 AN: 4764

European-Finnish (FIN) AF: 0.214 AC: 2162 AN: 10084

Middle Eastern (MID) AF: 0.207 AC: 60 AN: 290

European-Non Finnish (NFE) AF: 0.194 AC: 13110 AN: 67752

Other (OTH) AF: 0.178 AC: 372 AN: 2086

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

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.28
DANN	Benign	0.71
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8051232; hg19: chr16-19089562;