Genetic Variant STXBP6:c.154+10014_154+10017dupCACA (chr14-24964647-C-CTGTG) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001394410.1(STXBP6):c.154+10014_154+10017dupCACA 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 0.0069 ( 7 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1 link	c.154+10014_154+10017dupCACA		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+10018insCACA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5		Q8NFX7-1

Frequencies

GnomAD3 genomes

AF:

0.00687

AC:

962

AN:

140110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00697

Gnomad ASJ

AF:

0.00869

Gnomad EAS

AF:

0.0121

Gnomad SAS

AF:

0.00243

Gnomad FIN

AF:

0.0127

Gnomad MID

AF:

0.00338

Gnomad NFE

AF:

0.00311

Gnomad OTH

AF:

0.00685

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

GnomAD4 genome

AF:

0.00688

AC:

965

AN:

140194

Hom.:

Cov.:

AF XY:

0.00750

AC XY:

507

AN XY:

67622

show subpopulations

African (AFR)

AF:

0.0118

AC:

440

AN:

37288

American (AMR)

AF:

0.00696

AC:

AN:

13936

Ashkenazi Jewish (ASJ)

AF:

0.00869

AC:

AN:

3336

East Asian (EAS)

AF:

0.0124

AC:

AN:

4774

South Asian (SAS)

AF:

0.00269

AC:

AN:

4094

European-Finnish (FIN)

AF:

0.0127

AC:

114

AN:

8986

Middle Eastern (MID)

AF:

0.00368

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.00311

AC:

201

AN:

64710

Other (OTH)

AF:

0.00681

AC:

AN:

1908

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

119

159

199

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.045

Splicing

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

Publications

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14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTG

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