chr16-23445969-T-TAA

Variant names:

• chr16-23445969-T-TAA
• rs71379679
• NM_153603.4:c.170-10_170-9dupTT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_153603.4(COG7):​c.170-10_170-9dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,488,844 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000023 (0 hom., cov: 25)
  • Exomes 𝑓: 0.00054 (0 hom.)
• Consequence: COG7 NM_153603.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000544 (739/1359592) while in subpopulation AMR AF= 0.00148 (57/38502). AF 95% confidence interval is 0.00117. There are 0 homozygotes in gnomad4_exome. There are 366 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG7	NM_153603.4	c.170-10_170-9dupTT		intron_variant	Intron 1 of 16	ENST00000307149.10	NP_705831.1
COG7	XM_017023870.2	c.-26-10_-26-9dupTT		intron_variant	Intron 1 of 16		XP_016879359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG7	ENST00000307149.10	c.170-9_170-8insTT		intron_variant	Intron 1 of 16	1	NM_153603.4	ENSP00000305442.5

Frequencies

GnomAD3 genomes AF: 0.0000232 AC: 3 AN: 129252 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.0000286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000140

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000167

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000544 AC: 739 AN: 1359592 Hom.: 0 Cov.: 0 AF XY: 0.000540 AC XY: 366 AN XY: 677384

Gnomad4 AFR exome AF: 0.00107

Gnomad4 AMR exome AF: 0.00148

Gnomad4 ASJ exome AF: 0.000814

Gnomad4 EAS exome AF: 0.000265

Gnomad4 SAS exome AF: 0.000619

Gnomad4 FIN exome AF: 0.000458

Gnomad4 NFE exome AF: 0.000501

Gnomad4 OTH exome AF: 0.000478

GnomAD4 genome AF: 0.0000232 AC: 3 AN: 129252 Hom.: 0 Cov.: 25 AF XY: 0.0000322 AC XY: 2 AN XY: 62174

Gnomad4 AFR AF: 0.0000286

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000140

Gnomad4 NFE AF: 0.0000167

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71379679; hg19: chr16-23457290;