16-19078240-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016138.5(COQ7):​c.*82C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000883 in 1,018,886 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000033 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000046 (0 hom.)
• Consequence: COQ7 NM_016138.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0000332 AC: 5 AN: 150824 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000973

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000461 AC: 4 AN: 868062 Hom.: 0 Cov.: 11 AF XY: 0.00000224 AC XY: 1 AN XY: 445450

African (AFR) AF: 0.0000537 AC: 1 AN: 18606

American (AMR) AF: 0.00 AC: 0 AN: 24200

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18492

East Asian (EAS) AF: 0.00 AC: 0 AN: 31980

South Asian (SAS) AF: 0.0000523 AC: 3 AN: 57310

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47100

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4322

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 627000

Other (OTH) AF: 0.00 AC: 0 AN: 39052

GnomAD4 genome AF: 0.0000332 AC: 5 AN: 150824 Hom.: 0 Cov.: 31 AF XY: 0.0000408 AC XY: 3 AN XY: 73554

African (AFR) AF: 0.0000973 AC: 4 AN: 41090

American (AMR) AF: 0.00 AC: 0 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10092

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67782

Other (OTH) AF: 0.00 AC: 0 AN: 2070

Alfa AF: 0.0000660 Hom.: 226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.73
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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;