16-23388624-C-CT

Variant summary

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

The NM_153603.4(COG7):c.*295_*296insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.019 (44 hom., cov: 0)
  • Exomes 𝑓: 0.0025 (0 hom.)
• Consequence: COG7 NM_153603.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.557

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 -10 ACMG points.

• BP6: Variant 16-23388624-C-CT is Benign according to our data. Variant chr16-23388624-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 1203781.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0195 (2387/122436) while in subpopulation EAS AF= 0.0432 (181/4186). AF 95% confidence interval is 0.0381. There are 44 homozygotes in gnomad4. There are 1146 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COG7	NM_153603.4	c.*295_*296insA		3_prime_UTR_variant	17/17	ENST00000307149.10
COG7	XM_017023870.2	c.*295_*296insA		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG7	ENST00000307149.10	c.*295_*296insA		3_prime_UTR_variant	17/17	1	NM_153603.4	P1
COG7	ENST00000566364.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0195 AC: 2389 AN: 122426 Hom.: 44 Cov.: 0

Gnomad AFR AF: 0.00694

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0240

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0182

GnomAD4 exome AF: 0.00247 AC: 82 AN: 33230 Hom.: 0 Cov.: 0 AF XY: 0.00181 AC XY: 31 AN XY: 17112

Gnomad4 AFR exome AF: 0.00174

Gnomad4 AMR exome AF: 0.00649

Gnomad4 ASJ exome AF: 0.00226

Gnomad4 EAS exome AF: 0.000704

Gnomad4 SAS exome AF: 0.00184

Gnomad4 FIN exome AF: 0.00165

Gnomad4 NFE exome AF: 0.00266

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0195 AC: 2387 AN: 122436 Hom.: 44 Cov.: 0 AF XY: 0.0196 AC XY: 1146 AN XY: 58440

Gnomad4 AFR AF: 0.00690

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.0777

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.0192

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0181

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

Oct 12, 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: rs567617218; hg19: chr16-23399945;