chr16-69336355-G-A

Variant names:

• chr16-69336355-G-A
• rs715162
• NM_032382.5:c.585+150C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032382.5(COG8):​c.585+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 689,126 control chromosomes in the GnomAD database, including 1,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.057 (266 hom., cov: 32)
  • Exomes 𝑓: 0.058 (1056 hom.)
• Consequence: COG8 NM_032382.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.394
• Publications: 8 publications found

Genes affected

COG8 (HGNC:18623): (component of oligomeric golgi complex 8) This gene encodes a protein that is a component of the conserved oligomeric Golgi (COG) complex, a multiprotein complex that plays a structural role in the Golgi apparatus, and is involved in intracellular membrane trafficking and glycoprotein modification. Mutations in this gene cause congenital disorder of glycosylation, type IIh, a disease that is characterized by under-glycosylated serum proteins, and whose symptoms include severe psychomotor retardation, failure to thrive, seizures, and dairy and wheat product intolerance. [provided by RefSeq, Jul 2008]

COG8 Gene-Disease associations (from GenCC):

• COG8-congenital disorder of glycosylation

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000260371 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 16-69336355-G-A is Benign according to our data. Variant chr16-69336355-G-A is described in ClinVar as Benign. ClinVar VariationId is 1292132.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032382.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COG8	NM_032382.5	MANE Select	c.585+150C>T		intron	N/A	NP_115758.3
	COG8	NM_001379261.1		c.585+150C>T		intron	N/A	NP_001366190.1
	COG8	NM_001379262.1		c.585+150C>T		intron	N/A	NP_001366191.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COG8	ENST00000306875.10	TSL:1 MANE Select	c.585+150C>T		intron	N/A	ENSP00000305459.6
	ENSG00000260371	ENST00000563634.1	TSL:4	c.210+150C>T		intron	N/A	ENSP00000454500.1
	ENSG00000259900	ENST00000564737.1	TSL:5	n.*157+150C>T		intron	N/A	ENSP00000462747.1

Frequencies

GnomAD3 genomes AF: 0.0573 AC: 8722 AN: 152152 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0531

GnomAD4 exome AF: 0.0579 AC: 31099 AN: 536856 Hom.: 1056 AF XY: 0.0590 AC XY: 16631 AN XY: 282050

African (AFR) AF: 0.0623 AC: 871 AN: 13970

American (AMR) AF: 0.0505 AC: 1086 AN: 21494

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 744 AN: 14764

East Asian (EAS) AF: 0.0215 AC: 681 AN: 31700

South Asian (SAS) AF: 0.0775 AC: 3740 AN: 48280

European-Finnish (FIN) AF: 0.0349 AC: 1437 AN: 41140

Middle Eastern (MID) AF: 0.0456 AC: 100 AN: 2192

European-Non Finnish (NFE) AF: 0.0621 AC: 20781 AN: 334398

Other (OTH) AF: 0.0574 AC: 1659 AN: 28918

GnomAD4 genome AF: 0.0575 AC: 8752 AN: 152270 Hom.: 266 Cov.: 32 AF XY: 0.0562 AC XY: 4182 AN XY: 74452

African (AFR) AF: 0.0571 AC: 2372 AN: 41528

American (AMR) AF: 0.0604 AC: 924 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5190

South Asian (SAS) AF: 0.0817 AC: 395 AN: 4834

European-Finnish (FIN) AF: 0.0326 AC: 346 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4092 AN: 68032

Other (OTH) AF: 0.0591 AC: 125 AN: 2114

Alfa AF: 0.0599 Hom.: 189

Bravo AF: 0.0607

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.3
DANN	Benign	0.55
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs715162; hg19: chr16-69370258;