16-19067270-TAAAAA-T

Variant summary

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

The ENST00000666887.1(COQ7-DT):​n.158_162delTTTTT 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 0.000012 in 166,758 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 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000061 ( 0 hom. )

Consequence

COQ7-DT
ENST00000666887.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01
Variant links:
Genes affected
COQ7-DT (HGNC:55362): (COQ7 divergent transcript)

Genome browser will be placed here

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 HGVSp Effect Exon rank MANE Protein UniProt
COQ7-DTNR_119379.1 linkn.111+306_111+310delTTTTT intron_variant Intron 1 of 3
COQ7-DTNR_119380.1 linkn.141+276_141+280delTTTTT intron_variant Intron 1 of 2
COQ7-DTNR_119381.1 linkn.111+306_111+310delTTTTT intron_variant Intron 1 of 2
COQ7-DTNR_119382.1 linkn.166+43_166+47delTTTTT intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COQ7-DTENST00000666887.1 linkn.158_162delTTTTT non_coding_transcript_exon_variant Exon 1 of 3
COQ7-DTENST00000567047.1 linkn.111+306_111+310delTTTTT intron_variant Intron 1 of 2 2
COQ7-DTENST00000568971.5 linkn.91+276_91+280delTTTTT intron_variant Intron 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.00000665
AC:
1
AN:
150436
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000613
AC:
1
AN:
16322
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
9156
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000294
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000665
AC:
1
AN:
150436
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
73304
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000148
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000122
Hom.:
1608

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.

Other links and lift over

dbSNP: rs5816026; hg19: chr16-19078592; API