Variant 16-23388642-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_153603.4(COG7):c.*277del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0013 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

COG7
NM_153603.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.380

Variant links:

Genes affected

COG7 (HGNC:18622): (component of oligomeric golgi complex 7) The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the congenital disorder of glycosylation type IIe.[provided by RefSeq, May 2010]

COG7 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG7	NM_153603.4 linkuse as main transcript	c.*277del		3_prime_UTR_variant	17/17	ENST00000307149.10
COG7	XM_017023870.2 linkuse as main transcript	c.*277del		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG7	ENST00000307149.10 linkuse as main transcript	c.*277del		3_prime_UTR_variant	17/17	1	NM_153603.4	P1
COG7	ENST00000566364.1 linkuse as main transcript	n.937del		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

173

AN:

134002

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00270

Gnomad AMI

AF:

0.00116

Gnomad AMR

AF:

0.00169

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00198

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00219

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000408

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00130

AC:

AN:

37720

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

AN XY:

19182

show subpopulations

Gnomad4 AFR exome

AF:

0.00306

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.00136

Gnomad4 SAS exome

AF:

0.00171

Gnomad4 FIN exome

AF:

0.000987

Gnomad4 NFE exome

AF:

0.00133

Gnomad4 OTH exome

AF:

0.000838

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00132

AC:

177

AN:

134056

Hom.:

Cov.:

AF XY:

0.00140

AC XY:

AN XY:

65108

show subpopulations

Gnomad4 AFR

AF:

0.00278

Gnomad4 AMR

AF:

0.00168

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00198

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00219

Gnomad4 NFE

AF:

0.000408

Gnomad4 OTH

AF:

0.000535

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 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