14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant names:

• chr14-24964647-C-CTGTGTGTGTGTGTGTGTG
• rs34132743
• NM_001394410.1:c.154+10000_154+10017dupCACACACACACACACACA

Variant summary

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

The NM_001394410.1(STXBP6):​c.154+10000_154+10017dupCACACACACACACACACA 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 0.023 (95 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 (AFR) allele frequency at 95% confidence interval = 0.0535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+10000_154+10017dupCACACACACACACACACA		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+10018insCACACACACACACACACA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.0226 AC: 3163 AN: 139964 Hom.: 95 Cov.: 0

Gnomad AFR AF: 0.0555

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0339

Gnomad EAS AF: 0.0151

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.00111

Gnomad MID AF: 0.0135

Gnomad NFE AF: 0.00960

Gnomad OTH AF: 0.0274

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

GnomAD4 genome AF: 0.0226 AC: 3168 AN: 140046 Hom.: 95 Cov.: 0 AF XY: 0.0218 AC XY: 1471 AN XY: 67550

African (AFR) AF: 0.0555 AC: 2065 AN: 37206

American (AMR) AF: 0.0136 AC: 189 AN: 13928

Ashkenazi Jewish (ASJ) AF: 0.0339 AC: 113 AN: 3334

East Asian (EAS) AF: 0.0151 AC: 72 AN: 4766

South Asian (SAS) AF: 0.0103 AC: 42 AN: 4092

European-Finnish (FIN) AF: 0.00111 AC: 10 AN: 8978

Middle Eastern (MID) AF: 0.0147 AC: 4 AN: 272

European-Non Finnish (NFE) AF: 0.00960 AC: 621 AN: 64674

Other (OTH) AF: 0.0273 AC: 52 AN: 1906

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;