7-107297975-A-C

Position:

• chr7-107297975-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006348.5(COG5):​c.1313+167T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,114 control chromosomes in the GnomAD database, including 3,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (3184 hom., cov: 31)
• Consequence: COG5 NM_006348.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.900

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 7-107297975-A-C is Benign according to our data. Variant chr7-107297975-A-C is described in ClinVar as [Benign]. Clinvar id is 1237233.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COG5	NM_006348.5	c.1313+167T>G		intron_variant		ENST00000297135.9	NP_006339.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COG5	ENST00000297135.9	c.1313+167T>G		intron_variant		1	NM_006348.5	ENSP00000297135.4
COG5	ENST00000347053.8	c.1313+167T>G		intron_variant		1		ENSP00000334703.3
COG5	ENST00000393603.7	c.1313+167T>G		intron_variant		1		ENSP00000377228.3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30541 AN: 151996 Hom.: 3184 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.199

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30562 AN: 152114 Hom.: 3184 Cov.: 31 AF XY: 0.197 AC XY: 14627 AN XY: 74360

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.198

Alfa AF: 0.214 Hom.: 5503

Bravo AF: 0.205

Asia WGS AF: 0.182 AC: 632 AN: 3478

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

Sep 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.71

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: rs3815148; hg19: chr7-106938420;