chr16-23388642-TG-T

Position:

• chr16-23388642-TG-T

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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.380

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 173 AN: 134002 Hom.: 0 Cov.: 0 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: 49 AN: 37720 Hom.: 0 Cov.: 0 AF XY: 0.00146 AC XY: 28 AN XY: 19182

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.: 0 Cov.: 0 AF XY: 0.00140 AC XY: 91 AN XY: 65108

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

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

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

Other links and lift over

dbSNP: rs886051818; hg19: chr16-23399963;