16-19069336-T-G

Position:

• chr16-19069336-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016138.5(COQ7):​c.73+1599T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,514 control chromosomes in the GnomAD database, including 25,144 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (25144 hom., cov: 30)
• Consequence: COQ7 NM_016138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COQ7	NM_016138.5	c.73+1599T>G		intron_variant		ENST00000321998.10	NP_057222.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COQ7	ENST00000321998.10	c.73+1599T>G		intron_variant		1	NM_016138.5	ENSP00000322316.5

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84197 AN: 151392 Hom.: 25124 Cov.: 30

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.613

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.556 AC: 84258 AN: 151514 Hom.: 25144 Cov.: 30 AF XY: 0.564 AC XY: 41682 AN XY: 73928

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.613

Alfa AF: 0.456 Hom.: 1719

Bravo AF: 0.545

Asia WGS AF: 0.742 AC: 2579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.87

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: rs7192898; hg19: chr16-19080658;