chr2-197475052-A-G

Variant names:

• chr2-197475052-A-G
• rs11070
• NM_025147.5:c.*1128A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025147.5(COQ10B):​c.*1128A>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 0.171 in 152,202 control chromosomes in the GnomAD database, including 2,346 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 0.17 (2343 hom., cov: 31)
  • Exomes 𝑓: 0.25 (3 hom.)
• Consequence: COQ10B NM_025147.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 7 publications found

Genes affected

COQ10B (HGNC:25819): (coenzyme Q10B) Predicted to enable ubiquinone binding activity. Predicted to be involved in cellular respiration and ubiquinone biosynthetic process. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025147.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COQ10B	NM_025147.5	MANE Select	c.*1128A>G		3_prime_UTR	Exon 5 of 5	NP_079423.1
	COQ10B	NM_001320819.2		c.*1128A>G		3_prime_UTR	Exon 5 of 5	NP_001307748.1
	COQ10B	NM_001320820.2		c.*1128A>G		3_prime_UTR	Exon 5 of 5	NP_001307749.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COQ10B	ENST00000263960.7	TSL:1 MANE Select	c.*1128A>G		3_prime_UTR	Exon 5 of 5	ENSP00000263960.2
	COQ10B	ENST00000960457.1		c.*1128A>G		3_prime_UTR	Exon 5 of 5	ENSP00000630516.1
	COQ10B	ENST00000885461.1		c.*1128A>G		3_prime_UTR	Exon 4 of 4	ENSP00000555520.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25926 AN: 151946 Hom.: 2340 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.246 AC: 34 AN: 138 Hom.: 3 Cov.: 0 AF XY: 0.289 AC XY: 22 AN XY: 76

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.246 AC: 34 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.171 AC: 25956 AN: 152064 Hom.: 2343 Cov.: 31 AF XY: 0.171 AC XY: 12725 AN XY: 74304

African (AFR) AF: 0.119 AC: 4943 AN: 41484

American (AMR) AF: 0.197 AC: 3014 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 814 AN: 3472

East Asian (EAS) AF: 0.241 AC: 1244 AN: 5170

South Asian (SAS) AF: 0.119 AC: 574 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1944 AN: 10560

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12743 AN: 67966

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.176 Hom.: 576

Bravo AF: 0.173

Asia WGS AF: 0.175 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs11070; hg19: chr2-198339776;