Genetic Variant COQ7-DT:n.161_162delTT (chr16-19067270-TAA-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000666887.1(COQ7-DT):n.161_162delTT 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 0.00106 in 166,618 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000040 ( 0 hom., cov: 0)

Exomes 𝑓: 0.011 ( 0 hom. )

Consequence

COQ7-DT
ENST00000666887.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.998

Variant links:

Genes affected

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

COQ7-DT links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
COQ7-DT	NR_119379.1 link	n.111+309_111+310delTT	intron_variant	Intron 1 of 3
COQ7-DT	NR_119380.1 link	n.141+279_141+280delTT	intron_variant	Intron 1 of 2
COQ7-DT	NR_119381.1 link	n.111+309_111+310delTT	intron_variant	Intron 1 of 2
COQ7-DT	NR_119382.1 link	n.166+46_166+47delTT	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COQ7-DT	ENST00000666887.1 link	n.161_162delTT	non_coding_transcript_exon_variant	Exon 1 of 3
COQ7-DT	ENST00000567047.1 link	n.111+309_111+310delTT	intron_variant	Intron 1 of 2	2
COQ7-DT	ENST00000568971.5 link	n.91+279_91+280delTT	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0000399

AC:

AN:

150424

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000662

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000290

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0106

AC:

171

AN:

16096

Hom.:

AF XY:

0.0104

AC XY:

AN XY:

9048

show subpopulations

Gnomad4 AFR exome

AF:

0.00565

Gnomad4 AMR exome

AF:

0.00870

Gnomad4 ASJ exome

AF:

0.0103

Gnomad4 EAS exome

AF:

0.00694

Gnomad4 SAS exome

AF:

0.00832

Gnomad4 FIN exome

AF:

0.0121

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.0000399

AC:

AN:

150522

Hom.:

Cov.:

AF XY:

0.0000545

AC XY:

AN XY:

73410

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000662

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000290

Gnomad4 NFE

AF:

0.0000148

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

16-19067270-TAAAAA-TAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over