rs34132743

Variant names:

• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-C
• rs34132743
• NM_001394410.1:c.154+9998_154+10017delCACACACACACACACACACA

Your query was ambiguous. Multiple possible variants found:

• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-C
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001394410.1(STXBP6):​c.154+9998_154+10017delCACACACACACACACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 1 publications found

Genes affected

STXBP6 (HGNC:19666): (syntaxin binding protein 6) Enables cadherin binding activity involved in cell-cell adhesion. Predicted to be involved in Golgi to plasma membrane transport and exocytosis. Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394410.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	NM_001394410.1	MANE Select	c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	NP_001381339.1	Q8NFX7-1
	STXBP6	NM_001304476.3		c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	NP_001291405.1	Q8NFX7-1
	STXBP6	NM_001304477.3		c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	NP_001291406.1	Q8NFX7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	ENST00000323944.10	TSL:1 MANE Select	c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	ENSP00000324302.5	Q8NFX7-1
	STXBP6	ENST00000396700.5	TSL:1	c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	ENSP00000379928.1	Q8NFX7-1
	STXBP6	ENST00000419632.6	TSL:1	c.154+9998_154+10017delCACACACACACACACACACA		intron	N/A	ENSP00000397212.2	Q8NFX7-1

Frequencies

GnomAD3 genomes Cov.: 0

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs34132743; hg19: chr14-25433853;