rs715162

Positions:

• chr16-69336355-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000260371 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COG8	NM_032382.5	c.585+150C>T		intron_variant		ENST00000306875.10	NP_115758.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COG8	ENST00000306875.10	c.585+150C>T		intron_variant		1	NM_032382.5	ENSP00000305459.6
ENSG00000260371	ENST00000563634.1	c.210+150C>T		intron_variant		4		ENSP00000454500.1
ENSG00000259900	ENST00000564737.1	n.*157+150C>T		intron_variant		5		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

Gnomad4 AFR exome AF: 0.0623

Gnomad4 AMR exome AF: 0.0505

Gnomad4 ASJ exome AF: 0.0504

Gnomad4 EAS exome AF: 0.0215

Gnomad4 SAS exome AF: 0.0775

Gnomad4 FIN exome AF: 0.0349

Gnomad4 NFE exome AF: 0.0621

Gnomad4 OTH exome AF: 0.0574

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

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.0326

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0613 Hom.: 151

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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.3
DANN	Benign	0.55

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: rs715162; hg19: chr16-69370258;