rs71379679

chr16-23445969-TAAAAAA-Tchr16-23445969-TAAAAAA-TAAchr16-23445969-TAAAAAA-TAAAchr16-23445969-TAAAAAA-TAAAAchr16-23445969-TAAAAAA-TAAAAAchr16-23445969-TAAAAAA-TAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAAAAAchr16-23445969-TAAAAAA-TAAAAAAAAAAAAAAA

Variant summary

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

The NM_153603.4(COG7):c.170-14_170-9del variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000022 in 1,362,972 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: not found (cov: 25)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: COG7 NM_153603.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

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/exons	MANE	UniProt
COG7	NM_153603.4	c.170-14_170-9del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000307149.10
COG7	XM_017023870.2	c.-26-14_-26-9del		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COG7	ENST00000307149.10	c.170-14_170-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_153603.4	P1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 0.00000220 AC: 3 AN: 1362972 Hom.: 0 AF XY: 0.00000295 AC XY: 2 AN XY: 678998

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000519

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.53e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 25

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;