7-107563544-T-TG

Variant summary

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

The NM_006348.5(COG5):c.94+258_94+259insC 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 0.038 (139 hom., cov: 0)
  • Exomes 𝑓: 0.052 (2 hom.)
• Consequence: COG5 NM_006348.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.587

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 7-107563544-T-TG is Benign according to our data. Variant chr7-107563544-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 1190377.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG5	NM_006348.5	c.94+258_94+259insC		intron_variant		ENST00000297135.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG5	ENST00000297135.9	c.94+258_94+259insC		intron_variant		1	NM_006348.5	P2

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 2219 AN: 58616 Hom.: 139 Cov.: 0

Gnomad AFR AF: 0.00591

Gnomad AMI AF: 0.0729

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.00943

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0285

GnomAD4 exome AF: 0.0519 AC: 10124 AN: 195128 Hom.: 2 Cov.: 0 AF XY: 0.0546 AC XY: 5678 AN XY: 103970

Gnomad4 AFR exome AF: 0.0111

Gnomad4 AMR exome AF: 0.0421

Gnomad4 ASJ exome AF: 0.0407

Gnomad4 EAS exome AF: 0.0499

Gnomad4 SAS exome AF: 0.0695

Gnomad4 FIN exome AF: 0.0516

Gnomad4 NFE exome AF: 0.0514

Gnomad4 OTH exome AF: 0.0497

GnomAD4 genome AF: 0.0376 AC: 2209 AN: 58676 Hom.: 139 Cov.: 0 AF XY: 0.0394 AC XY: 1083 AN XY: 27486

Gnomad4 AFR AF: 0.00589

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0284

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 14, 2020

- -

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: rs71134268; hg19: chr7-107203989;