14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTG

Position:

• chr14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001394410.1(STXBP6):​c.154+10016_154+10017delCA 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 0.068 (617 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+10016_154+10017delCA		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+10016_154+10017delCA		intron_variant		1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 9457 AN: 139556 Hom.: 616 Cov.: 0

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0372

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0165

Gnomad EAS AF: 0.00356

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0236

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0679 AC: 9477 AN: 139630 Hom.: 617 Cov.: 0 AF XY: 0.0680 AC XY: 4574 AN XY: 67302

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.0165

Gnomad4 EAS AF: 0.00377

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0370

Gnomad4 NFE AF: 0.0242

Gnomad4 OTH AF: 0.0527

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: rs34132743; hg19: chr14-25433853;