16-19067270-TA-T

Variant names:

• chr16-19067270-TA-T
• rs5816026
• ENST00000666887.1:n.162delT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000666887.1(COQ7-DT):​n.162delT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.65 (32920 hom., cov: 0)
  • Exomes 𝑓: 0.64 (3114 hom.)
• Consequence: COQ7-DT ENST00000666887.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.998

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-19067270-TA-T is Benign according to our data. Variant chr16-19067270-TA-T is described in ClinVar as [Benign]. Clinvar id is 1267344.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COQ7-DT	NR_119379.1	n.111+310delT		intron_variant	Intron 1 of 3
COQ7-DT	NR_119380.1	n.141+280delT		intron_variant	Intron 1 of 2
COQ7-DT	NR_119381.1	n.111+310delT		intron_variant	Intron 1 of 2
COQ7-DT	NR_119382.1	n.166+47delT		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COQ7-DT	ENST00000666887.1	n.162delT		non_coding_transcript_exon_variant	Exon 1 of 3
COQ7-DT	ENST00000567047.1	n.111+310delT		intron_variant	Intron 1 of 2	2
COQ7-DT	ENST00000568971.5	n.91+280delT		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.650 AC: 97758 AN: 150348 Hom.: 32895 Cov.: 0

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.666

GnomAD4 exome AF: 0.638 AC: 10337 AN: 16198 Hom.: 3114 Cov.: 0 AF XY: 0.641 AC XY: 5818 AN XY: 9078

Gnomad4 AFR exome AF: 0.446

Gnomad4 AMR exome AF: 0.585

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.695

Gnomad4 SAS exome AF: 0.645

Gnomad4 FIN exome AF: 0.672

Gnomad4 NFE exome AF: 0.651

Gnomad4 OTH exome AF: 0.616

GnomAD4 genome AF: 0.650 AC: 97819 AN: 150446 Hom.: 32920 Cov.: 0 AF XY: 0.653 AC XY: 47904 AN XY: 73376

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.661

Bravo AF: 0.631

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 15, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5816026; hg19: chr16-19078592;