Genetic Variant STXBP6:c.154+10016_154+10017dupCA (chr14-24964647-C-CTG) – 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+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

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1 link	c.154+10016_154+10017dupCA		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+10018insCA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5		Q8NFX7-1

Frequencies

GnomAD3 genomes

AF:

0.0459

AC:

6427

AN:

140064

Hom.:

157

Cov.:

show subpopulations

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.:

AF XY:

0.0445

AC XY:

3011

AN XY:

67610

show subpopulations

African (AFR)

AF:

0.0322

AC:

1199

AN:

37288

American (AMR)

AF:

0.0340

AC:

473

AN:

13928

Ashkenazi Jewish (ASJ)

AF:

0.0456

AC:

152

AN:

3334

East Asian (EAS)

AF:

0.0388

AC:

185

AN:

4774

South Asian (SAS)

AF:

0.0437

AC:

179

AN:

4094

European-Finnish (FIN)

AF:

0.0465

AC:

418

AN:

8980

Middle Eastern (MID)

AF:

0.0441

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.0566

AC:

3659

AN:

64678

Other (OTH)

AF:

0.0482

AC:

AN:

1910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

273

547

820

1094

1367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<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:

0.0274

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTG

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