14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Position:

• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

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

The NM_001394410.1(STXBP6):​c.154+9996_154+10017dupCACACACACACACACACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0016 (0 hom., cov: 0)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+9996_154+10017dupCACACACACACACACACACACA		intron_variant		ENST00000323944.10	NP_001381339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STXBP6	ENST00000323944.10	c.154+9996_154+10017dupCACACACACACACACACACACA		intron_variant		1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.00161 AC: 225 AN: 140110 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.000600

Gnomad EAS AF: 0.000835

Gnomad SAS AF: 0.00170

Gnomad FIN AF: 0.000111

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000989

Gnomad OTH AF: 0.00158

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

GnomAD4 genome AF: 0.00160 AC: 225 AN: 140194 Hom.: 0 Cov.: 0 AF XY: 0.00170 AC XY: 115 AN XY: 67624

Gnomad4 AFR AF: 0.00330

Gnomad4 AMR AF: 0.00151

Gnomad4 ASJ AF: 0.000600

Gnomad4 EAS AF: 0.000838

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.000111

Gnomad4 NFE AF: 0.000989

Gnomad4 OTH AF: 0.00157

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: rs34132743; hg19: chr14-25433853;