Variant chr13-39655705-A-AG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_020751.3(COG6):c.-17dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,579,008 control chromosomes in the GnomAD database, including 133,674 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 12707 hom., cov: 0)

Exomes 𝑓: 0.41 ( 120967 hom. )

Consequence

COG6
NM_020751.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.35

Variant links:

Genes affected

COG6 (HGNC:18621): (component of oligomeric golgi complex 6) This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi apparatus. The encoded protein is organized with conserved oligomeric Golgi complex components 5, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]

COG6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 13-39655705-A-AG is Benign according to our data. Variant chr13-39655705-A-AG is described in ClinVar as [Likely_benign]. Clinvar id is 193435.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
COG6	NM_020751.3 linkuse as main transcript	c.-17dup	5_prime_UTR_variant	1/19	ENST00000455146.8
COG6	NM_001145079.2 linkuse as main transcript	c.-17dup	5_prime_UTR_variant	1/19
COG6	XM_011535168.2 linkuse as main transcript	c.-17dup	5_prime_UTR_variant	1/20
COG6	NR_026745.1 linkuse as main transcript	n.84dup	non_coding_transcript_exon_variant	1/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG6	ENST00000455146.8 linkuse as main transcript	c.-17dup		5_prime_UTR_variant	1/19	1	NM_020751.3	P1	Q9Y2V7-1

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61199

AN:

152004

Hom.:

12690

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.521

Gnomad FIN

AF:

0.362

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.384

Gnomad OTH

AF:

0.450

GnomAD3 exomes

AF:

0.456

AC:

88241

AN:

193390

Hom.:

21168

AF XY:

0.455

AC XY:

47948

AN XY:

105324

show subpopulations

Gnomad AFR exome

AF:

0.348

Gnomad AMR exome

AF:

0.647

Gnomad ASJ exome

AF:

0.470

Gnomad EAS exome

AF:

0.437

Gnomad SAS exome

AF:

0.547

Gnomad FIN exome

AF:

0.364

Gnomad NFE exome

AF:

0.391

Gnomad OTH exome

AF:

0.451

GnomAD4 exome

AF:

0.406

AC:

579521

AN:

1426886

Hom.:

120967

Cov.:

AF XY:

0.410

AC XY:

289970

AN XY:

706776

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.635

Gnomad4 ASJ exome

AF:

0.471

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.546

Gnomad4 FIN exome

AF:

0.366

Gnomad4 NFE exome

AF:

0.385

Gnomad4 OTH exome

AF:

0.420

GnomAD4 genome

AF:

0.403

AC:

61245

AN:

152122

Hom.:

12707

Cov.:

AF XY:

0.407

AC XY:

30289

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.354

Gnomad4 AMR

AF:

0.567

Gnomad4 ASJ

AF:

0.458

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.522

Gnomad4 FIN

AF:

0.362

Gnomad4 NFE

AF:

0.384

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.395

Hom.:

2219

Bravo

AF:

0.416

Asia WGS

AF:

0.502

AC:

1745

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Oct 14, 2014

- -

Congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 08, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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