Genetic Variant ENST00000666887.1:n.125T>A (chr16-19067308-A-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000666887.1(COQ7-DT):n.125T>A 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 0.13 in 225,936 control chromosomes in the GnomAD database, including 2,203 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1451 hom., cov: 33)

Exomes 𝑓: 0.12 ( 752 hom. )

Consequence

COQ7-DT
ENST00000666887.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0920

Variant links:

Genes affected

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

COQ7-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 16-19067308-A-T is Benign according to our data. Variant chr16-19067308-A-T is described in ClinVar as [Benign]. Clinvar id is 669474.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
COQ7-DT	NR_119379.1 link	n.111+273T>A	intron_variant	Intron 1 of 3
COQ7-DT	NR_119380.1 link	n.141+243T>A	intron_variant	Intron 1 of 2
COQ7-DT	NR_119381.1 link	n.111+273T>A	intron_variant	Intron 1 of 2
COQ7-DT	NR_119382.1 link	n.166+10T>A	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COQ7-DT	ENST00000666887.1 link	n.125T>A	non_coding_transcript_exon_variant	Exon 1 of 3
COQ7-DT	ENST00000567047.1 link	n.111+273T>A	intron_variant	Intron 1 of 2	2
COQ7-DT	ENST00000568971.5 link	n.91+243T>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20241

AN:

152066

Hom.:

1447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0933

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.0985

GnomAD4 exome

AF:

0.125

AC:

9185

AN:

73752

Hom.:

752

Cov.:

AF XY:

0.129

AC XY:

5008

AN XY:

38802

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.0958

Gnomad4 ASJ exome

AF:

0.0949

Gnomad4 EAS exome

AF:

0.000710

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.0995

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.133

AC:

20263

AN:

152184

Hom.:

1451

Cov.:

AF XY:

0.129

AC XY:

9619

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.0933

Gnomad4 ASJ

AF:

0.108

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.0970

Alfa

AF:

0.135

Hom.:

159

Bravo

AF:

0.131

Asia WGS

AF:

0.0820

AC:

286

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

7.2

DANN

Benign

0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over