14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant names:

• chr14-24964647-C-CTGTGTGTGTGTGTGTG
• rs34132743
• NM_001394410.1:c.154+10002_154+10017dupCACACACACACACACA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001394410.1(STXBP6):​c.154+10002_154+10017dupCACACACACACACACA 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 INS_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: 𝑓 0.025 (58 hom., cov: 0)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+10002_154+10017dupCACACACACACACACA		intron_variant	Intron 2 of 5	ENST00000323944.10	NP_001381339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP6	ENST00000323944.10	c.154+10017_154+10018insCACACACACACACACA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3440 AN: 140004 Hom.: 58 Cov.: 0

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.00337

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0348

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.00757

Gnomad MID AF: 0.0507

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0245 AC: 3436 AN: 140088 Hom.: 58 Cov.: 0 AF XY: 0.0240 AC XY: 1623 AN XY: 67574

African (AFR) AF: 0.0233 AC: 868 AN: 37244

American (AMR) AF: 0.0218 AC: 304 AN: 13922

Ashkenazi Jewish (ASJ) AF: 0.0348 AC: 116 AN: 3332

East Asian (EAS) AF: 0.0337 AC: 161 AN: 4772

South Asian (SAS) AF: 0.0575 AC: 235 AN: 4086

European-Finnish (FIN) AF: 0.00757 AC: 68 AN: 8982

Middle Eastern (MID) AF: 0.0478 AC: 13 AN: 272

European-Non Finnish (NFE) AF: 0.0250 AC: 1618 AN: 64680

Other (OTH) AF: 0.0262 AC: 50 AN: 1908

Alfa AF: 0.00 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.045
Mutation Taster		=100/0	polymorphism

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;