16-23388624-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_153603.4(COG7):c.*295del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (2694 hom., cov: 0)
  • Exomes 𝑓: 0.024 (0 hom.)
• Consequence: COG7 NM_153603.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.557

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 Benign. Variant got -16 ACMG points.

• BP6: Variant 16-23388624-CT-C is Benign according to our data. Variant chr16-23388624-CT-C is described in ClinVar as [Benign]. Clinvar id is 318455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG7	NM_153603.4	c.*295del		3_prime_UTR_variant	17/17	ENST00000307149.10
COG7	XM_017023870.2	c.*295del		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG7	ENST00000307149.10	c.*295del		3_prime_UTR_variant	17/17	1	NM_153603.4	P1
COG7	ENST00000566364.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 30922 AN: 122012 Hom.: 2691 Cov.: 0

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.0240 AC: 796 AN: 33198 Hom.: 0 Cov.: 0 AF XY: 0.0236 AC XY: 404 AN XY: 17086

Gnomad4 AFR exome AF: 0.0243

Gnomad4 AMR exome AF: 0.0450

Gnomad4 ASJ exome AF: 0.0113

Gnomad4 EAS exome AF: 0.0113

Gnomad4 SAS exome AF: 0.0242

Gnomad4 FIN exome AF: 0.0247

Gnomad4 NFE exome AF: 0.0233

Gnomad4 OTH exome AF: 0.0239

GnomAD4 genome AF: 0.253 AC: 30932 AN: 122022 Hom.: 2694 Cov.: 0 AF XY: 0.254 AC XY: 14800 AN XY: 58244

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.238

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Aug 06, 2019

- -

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: rs567617218; hg19: chr16-23399945;