Genetic Variant NM_025147.5:c.*1128A>G (chr2-197475052-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Publications

7 publications found

Variant links:

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]

COQ10B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
COQ10B	NM_025147.5 link	c.*1128A>G	3_prime_UTR_variant	Exon 5 of 5	ENST00000263960.7	NP_079423.1	Q9H8M1-1
COQ10B	NM_001320819.2 link	c.*1128A>G	3_prime_UTR_variant	Exon 5 of 5		NP_001307748.1	Q9H8M1B8ZZV9
COQ10B	NM_001320820.2 link	c.*1128A>G	3_prime_UTR_variant	Exon 5 of 5		NP_001307749.1	Q9H8M1-2
COQ10B	NM_001320818.2 link	c.*1128A>G	3_prime_UTR_variant	Exon 4 of 4		NP_001307747.1	Q9H8M1B8ZZX2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COQ10B	ENST00000263960.7 link	c.*1128A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_025147.5	ENSP00000263960.2		Q9H8M1-1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25926

AN:

151946

Hom.:

2340

Cov.:

show subpopulations

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:

AN:

138

Hom.:

Cov.:

AF XY:

0.289

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.246

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.171

AC:

25956

AN:

152064

Hom.:

2343

Cov.:

AF XY:

0.171

AC XY:

12725

AN XY:

74304

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12743

AN:

67966

Other (OTH)

AF:

0.198

AC:

418

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1106

2212

3317

4423

5529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over