16-23451984-C-G

Position:

• chr16-23451984-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153603.4(COG7):​c.169+842G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,974 control chromosomes in the GnomAD database, including 2,431 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2431 hom., cov: 32)
• Consequence: COG7 NM_153603.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

COG7 (HGNC:18622): (component of oligomeric golgi complex 7) The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the congenital disorder of glycosylation type IIe.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG7	NM_153603.4	c.169+842G>C		intron_variant		ENST00000307149.10
COG7	XM_017023870.2	c.-27+759G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG7	ENST00000307149.10	c.169+842G>C		intron_variant		1	NM_153603.4	P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26659 AN: 151856 Hom.: 2428 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.176 AC: 26685 AN: 151974 Hom.: 2431 Cov.: 32 AF XY: 0.179 AC XY: 13312 AN XY: 74278

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.167

Alfa AF: 0.170 Hom.: 286

Bravo AF: 0.170

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.36

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: rs394908; hg19: chr16-23463305;