Genetic Variant STXBP6:c.154+10012_154+10017dupCACACA (chr14-24964647-C-CTGTGTG) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The NM_001394410.1(STXBP6):c.154+10012_154+10017dupCACACA 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 0.057 ( 401 hom., cov: 0)

Consequence

STXBP6
NM_001394410.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0450

Publications

1 publications found

Variant links:

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]

STXBP6 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1 link	c.154+10012_154+10017dupCACACA		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 link	c.154+10017_154+10018insCACACA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5		Q8NFX7-1

Frequencies

GnomAD3 genomes

AF:

0.0571

AC:

8002

AN:

140062

Hom.:

402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.0809

Gnomad AMR

AF:

0.0374

Gnomad ASJ

AF:

0.0543

Gnomad EAS

AF:

0.0719

Gnomad SAS

AF:

0.0407

Gnomad FIN

AF:

0.00979

Gnomad MID

AF:

0.0845

Gnomad NFE

AF:

0.0259

Gnomad OTH

AF:

0.0526

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

GnomAD4 genome

AF:

0.0571

AC:

8002

AN:

140146

Hom.:

401

Cov.:

AF XY:

0.0556

AC XY:

3756

AN XY:

67606

show subpopulations

African (AFR)

AF:

0.130

AC:

4840

AN:

37244

American (AMR)

AF:

0.0373

AC:

520

AN:

13934

Ashkenazi Jewish (ASJ)

AF:

0.0543

AC:

181

AN:

3336

East Asian (EAS)

AF:

0.0716

AC:

342

AN:

4774

South Asian (SAS)

AF:

0.0398

AC:

163

AN:

4094

European-Finnish (FIN)

AF:

0.00979

AC:

AN:

8986

Middle Eastern (MID)

AF:

0.0809

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.0259

AC:

1674

AN:

64706

Other (OTH)

AF:

0.0524

AC:

100

AN:

1910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

320

640

959

1279

1599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00819

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.045

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over