7-107563546-G-GC

Position:

• chr7-107563546-G-GC

Variant summary

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

The NM_006348.5(COG5):​c.94+256_94+257insG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.18 (1092 hom., cov: 14)
  • Exomes 𝑓: 0.27 (374 hom.)
• Consequence: COG5 NM_006348.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.150

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 7-107563546-G-GC is Benign according to our data. Variant chr7-107563546-G-GC is described in ClinVar as [Benign]. Clinvar id is 1281977.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG5	NM_006348.5	c.94+256_94+257insG		intron_variant		ENST00000297135.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG5	ENST00000297135.9	c.94+256_94+257insG		intron_variant		1	NM_006348.5	P2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 11336 AN: 61432 Hom.: 1098 Cov.: 14

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.268 AC: 33116 AN: 123768 Hom.: 374 Cov.: 1 AF XY: 0.267 AC XY: 17701 AN XY: 66196

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.274

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.259

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.221

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.267

GnomAD4 genome AF: 0.184 AC: 11314 AN: 61378 Hom.: 1092 Cov.: 14 AF XY: 0.179 AC XY: 5272 AN XY: 29474

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.177

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

Oct 29, 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: rs34924876; hg19: chr7-107203991;