chr14-24964647-C-CTG

Position:

• chr14-24964647-C-CTG

Variant summary

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

The NM_001394410.1(STXBP6):​c.154+10016_154+10017dupCA 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 0.046 (157 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 (NFE) allele frequency at 95% confidence interval = 0.055 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+10017dupCA		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+10017dupCA		intron_variant		1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6427 AN: 140064 Hom.: 157 Cov.: 0

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.0730

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0456

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.0438

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0405

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0459 AC: 6434 AN: 140148 Hom.: 157 Cov.: 0 AF XY: 0.0445 AC XY: 3011 AN XY: 67610

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0456

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0482

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;