13-39724501-T-TA

Position:

• chr13-39724501-T-TA

Variant summary

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

The ENST00000455146.8(COG6):​c.1693-4dup variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: COG6 ENST00000455146.8 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

Genes affected

COG6 (HGNC:18621): (component of oligomeric golgi complex 6) This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi apparatus. The encoded protein is organized with conserved oligomeric Golgi complex components 5, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COG6	NM_020751.3	c.1693-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000455146.8	NP_065802.1
COG6	NM_001145079.2	c.1693-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NP_001138551.1
COG6	XM_011535168.2	c.1693-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			XP_011533470.1
COG6	NR_026745.1	n.1858-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COG6	ENST00000455146.8	c.1693-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_020751.3	ENSP00000397441	P1
COG6	ENST00000416691.5	c.1693-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000403733
COG6	ENST00000356576.8	c.*1530-4dup		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		1		ENSP00000348983

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 16

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs66629036; hg19: chr13-40298638;