7-107563543-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_006348.5(COG5):c.94+259del 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 0.016 (2 hom., cov: 8)
  • Exomes 𝑓: 0.015 (50 hom.)
• Consequence: COG5 NM_006348.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.216

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 7-107563543-AT-A is Benign according to our data. Variant chr7-107563543-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 1178744.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0158 (179/11314) while in subpopulation AFR AF= 0.0308 (117/3804). AF 95% confidence interval is 0.0262. There are 2 homozygotes in gnomad4. There are 80 alleles in male gnomad4 subpopulation. Median coverage is 8. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0158 AC: 179 AN: 11314 Hom.: 2 Cov.: 8

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00613

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00649

Gnomad OTH AF: 0.0259

GnomAD4 exome AF: 0.0151 AC: 4586 AN: 303482 Hom.: 50 Cov.: 0 AF XY: 0.0149 AC XY: 2410 AN XY: 161252

Gnomad4 AFR exome AF: 0.00554

Gnomad4 AMR exome AF: 0.00997

Gnomad4 ASJ exome AF: 0.00571

Gnomad4 EAS exome AF: 0.000213

Gnomad4 SAS exome AF: 0.0106

Gnomad4 FIN exome AF: 0.0219

Gnomad4 NFE exome AF: 0.0189

Gnomad4 OTH exome AF: 0.0135

GnomAD4 genome AF: 0.0158 AC: 179 AN: 11314 Hom.: 2 Cov.: 8 AF XY: 0.0150 AC XY: 80 AN XY: 5320

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.0113

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00613

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.00650

Gnomad4 OTH AF: 0.0259

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

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1230375721; hg19: chr7-107203988;