Genetic Variant NM_001394410.1:c.154+10016_154+10017delCA (chr14-24964647-CTG-C) – 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+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

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 (AFR) allele frequency at 95% confidence interval = 0.177 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+10017delCA		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+10016_154+10017delCA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5		Q8NFX7-1

Frequencies

GnomAD3 genomes

AF:

0.0678

AC:

9457

AN:

139556

Hom.:

616

Cov.:

show subpopulations

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.:

AF XY:

0.0680

AC XY:

4574

AN XY:

67302

show subpopulations

African (AFR)

AF:

0.180

AC:

6714

AN:

37222

American (AMR)

AF:

0.0416

AC:

578

AN:

13886

Ashkenazi Jewish (ASJ)

AF:

0.0165

AC:

AN:

3332

East Asian (EAS)

AF:

0.00377

AC:

AN:

4770

South Asian (SAS)

AF:

0.0213

AC:

AN:

4084

European-Finnish (FIN)

AF:

0.0370

AC:

323

AN:

8740

Middle Eastern (MID)

AF:

0.0259

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.0242

AC:

1562

AN:

64542

Other (OTH)

AF:

0.0527

AC:

100

AN:

1896

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

356

712

1068

1424

1780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0215

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

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

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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