rs397756552

Variant names:

• chr13-39679963-AT-A
• rs397756552
• NM_020751.3:c.624-3delT

Your query was ambiguous. Multiple possible variants found:

• chr13-39679963-AT-A
• chr13-39679963-AT-ATT
• chr13-39679963-AT-ATTT

Variant summary

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

The NM_020751.3(COG6):​c.624-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000406 in 1,390,130 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.0000066 (0 hom., cov: 21)
  • Exomes 𝑓: 0.00046 (0 hom.)
• Consequence: COG6 NM_020751.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

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 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
COG6	NM_020751.3	c.624-3delT		splice_region_variant, intron_variant	Intron 6 of 18	ENST00000455146.8	NP_065802.1
COG6	NM_001145079.2	c.624-3delT		splice_region_variant, intron_variant	Intron 6 of 18		NP_001138551.1
COG6	XM_011535168.2	c.624-3delT		splice_region_variant, intron_variant	Intron 6 of 19		XP_011533470.1
COG6	NR_026745.1	n.789-3delT		splice_region_variant, intron_variant	Intron 7 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG6	ENST00000455146.8	c.624-3delT		splice_region_variant, intron_variant	Intron 6 of 18	1	NM_020751.3	ENSP00000397441.2

Frequencies

GnomAD3 genomes AF: 0.00000660 AC: 1 AN: 151474 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

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: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000455 AC: 564 AN: 1238656 Hom.: 0 Cov.: 20 AF XY: 0.000436 AC XY: 273 AN XY: 626076

Gnomad4 AFR exome AF: 0.000319

Gnomad4 AMR exome AF: 0.0000690

Gnomad4 ASJ exome AF: 0.000244

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000217

Gnomad4 FIN exome AF: 0.0000191

Gnomad4 NFE exome AF: 0.000554

Gnomad4 OTH exome AF: 0.000362

GnomAD4 genome AF: 0.00000660 AC: 1 AN: 151474 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 73948

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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: rs397756552; hg19: chr13-40254100;