dbSNP rs150579326: COQ7-DT:n.35A>G (chr16-19067449-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_119382.1(COQ7-DT):n.35A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 558,932 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 5 hom., cov: 33)

Exomes 𝑓: 0.00045 ( 1 hom. )

Consequence

COQ7-DT
NR_119382.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.214

Publications

0 publications found

Variant links:

Genes affected

COQ7-DT (HGNC:55362): (COQ7 divergent transcript)

COQ7-DT links:

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 Gene-Disease associations (from GenCC):

primary coenzyme Q10 deficiency 8
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

COQ7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 16-19067449-T-C is Benign according to our data. Variant chr16-19067449-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1316957.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_119382.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
COQ7-DT	NR_119382.1	n.35A>G	non_coding_transcript_exon	Exon 1 of 3
COQ7-DT	NR_119379.1	n.111+132A>G	intron	N/A
COQ7-DT	NR_119380.1	n.141+102A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
COQ7-DT	ENST00000567047.2	TSL:2	n.192+132A>G	intron	N/A
COQ7-DT	ENST00000568971.5	TSL:2	n.91+102A>G	intron	N/A
COQ7-DT	ENST00000571934.5	TSL:5	n.91+102A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00423

AC:

643

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0150

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000957

GnomAD4 exome

AF:

0.000450

AC:

183

AN:

406642

Hom.:

Cov.:

AF XY:

0.000335

AC XY:

AN XY:

214658

show subpopulations

African (AFR)

AF:

0.0151

AC:

137

AN:

9070

American (AMR)

AF:

0.00148

AC:

AN:

12154

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12366

East Asian (EAS)

AF:

0.00

AC:

AN:

25532

South Asian (SAS)

AF:

0.0000737

AC:

AN:

40712

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29522

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2398

European-Non Finnish (NFE)

AF:

0.0000279

AC:

AN:

251196

Other (OTH)

AF:

0.000760

AC:

AN:

23692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.00426

AC:

648

AN:

152290

Hom.:

Cov.:

AF XY:

0.00404

AC XY:

301

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0150

AC:

625

AN:

41566

American (AMR)

AF:

0.00124

AC:

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.000414

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68014

Other (OTH)

AF:

0.000947

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

113

150

188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.00319

Hom.:

Bravo

AF:

0.00482

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

2.9

(source)

DANN

Benign

0.61

PhyloP100

-0.21

PromoterAI

-0.021

Neutral

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over