2-197475052-A-G

Position:

• chr2-197475052-A-G

Variant summary

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

The ENST00000263960.7(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 ENST00000263960.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COQ10B	NM_025147.5	c.*1128A>G		3_prime_UTR_variant	5/5	ENST00000263960.7	NP_079423.1
COQ10B	NM_001320818.2	c.*1128A>G		3_prime_UTR_variant	4/4		NP_001307747.1
COQ10B	NM_001320819.2	c.*1128A>G		3_prime_UTR_variant	5/5		NP_001307748.1
COQ10B	NM_001320820.2	c.*1128A>G		3_prime_UTR_variant	5/5		NP_001307749.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COQ10B	ENST00000263960.7	c.*1128A>G		3_prime_UTR_variant	5/5	1	NM_025147.5	ENSP00000263960	P1

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

Gnomad4 EAS exome AF: 0.246

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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.198

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11070; hg19: chr2-198339776;