7-107563545-G-GGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006348.5(COG5):c.94+257_94+258insGC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.083 (176 hom., cov: 0)
  • Exomes 𝑓: 0.18 (34 hom.)
  • Failed GnomAD Quality Control
• Consequence: COG5 NM_006348.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.29

Genes affected

COG5 (HGNC:14857): (component of oligomeric golgi complex 5) The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. The encoded protein is organized with conserved oligomeric Golgi complex components 6, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants. Mutations in this gene result in congenital disorder of glycosylation type 2I.[provided by RefSeq, Jan 2011]

DUS4L (HGNC:21517): (dihydrouridine synthase 4 like) Predicted to enable tRNA dihydrouridine synthase activity. Predicted to be involved in tRNA dihydrouridine synthesis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-107563545-G-GGC is Benign according to our data. Variant chr7-107563545-G-GGC is described in ClinVar as [Likely_benign]. Clinvar id is 1215761.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG5	NM_006348.5	c.94+257_94+258insGC		intron_variant		ENST00000297135.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG5	ENST00000297135.9	c.94+257_94+258insGC		intron_variant		1	NM_006348.5	P2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2507 AN: 30316 Hom.: 176 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0236

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.180 AC: 7580 AN: 41996 Hom.: 34 Cov.: 0 AF XY: 0.181 AC XY: 4057 AN XY: 22434

Gnomad4 AFR exome AF: 0.198

Gnomad4 AMR exome AF: 0.148

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.0117

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0828 AC: 2508 AN: 30302 Hom.: 176 Cov.: 0 AF XY: 0.0799 AC XY: 1130 AN XY: 14146

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.0684

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0271

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0952

Gnomad4 OTH AF: 0.112

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 13, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1554466263; hg19: chr7-107203990;