16-23445969-TAAAAAA-TAAAAAAAAA

Variant names:

• chr16-23445969-T-TAAA
• rs71379679
• NM_153603.4:c.170-11_170-9dupTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_153603.4(COG7):​c.170-11_170-9dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000811 in 1,491,906 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 0.000054 (0 hom., cov: 25)
  • Exomes 𝑓: 0.000084 (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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG7	NM_153603.4	c.170-11_170-9dupTTT		intron_variant	Intron 1 of 16	ENST00000307149.10	NP_705831.1
COG7	XM_017023870.2	c.-26-11_-26-9dupTTT		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_170-8insTTT		intron_variant	Intron 1 of 16	1	NM_153603.4	ENSP00000305442.5

Frequencies

GnomAD3 genomes AF: 0.0000542 AC: 7 AN: 129242 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.0000286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000792

Gnomad ASJ AF: 0.000322

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000140

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000501

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000837 AC: 114 AN: 1362664 Hom.: 0 Cov.: 0 AF XY: 0.0000722 AC XY: 49 AN XY: 678842

Gnomad4 AFR exome AF: 0.000133

Gnomad4 AMR exome AF: 0.000389

Gnomad4 ASJ exome AF: 0.000284

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000164

Gnomad4 FIN exome AF: 0.000120

Gnomad4 NFE exome AF: 0.0000610

Gnomad4 OTH exome AF: 0.0000883

GnomAD4 genome AF: 0.0000542 AC: 7 AN: 129242 Hom.: 0 Cov.: 25 AF XY: 0.0000322 AC XY: 2 AN XY: 62170

Gnomad4 AFR AF: 0.0000286

Gnomad4 AMR AF: 0.0000792

Gnomad4 ASJ AF: 0.000322

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000140

Gnomad4 NFE AF: 0.0000501

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;