rs10147992

Variant names:

• chr14-25034593-A-G
• rs10147992
• NM_001394410.1:c.-33+15285T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-25034593-A-G
• chr14-25034593-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394410.1(STXBP6):​c.-33+15285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,976 control chromosomes in the GnomAD database, including 19,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (19562 hom., cov: 31)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 14 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394410.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	NM_001394410.1	MANE Select	c.-33+15285T>C		intron	N/A	NP_001381339.1	Q8NFX7-1
	STXBP6	NM_001304476.3		c.-149+15285T>C		intron	N/A	NP_001291405.1	Q8NFX7-1
	STXBP6	NM_001304477.3		c.-33+14367T>C		intron	N/A	NP_001291406.1	Q8NFX7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	ENST00000323944.10	TSL:1 MANE Select	c.-33+15285T>C		intron	N/A	ENSP00000324302.5	Q8NFX7-1
	STXBP6	ENST00000396700.5	TSL:1	c.-149+15285T>C		intron	N/A	ENSP00000379928.1	Q8NFX7-1
	STXBP6	ENST00000419632.6	TSL:1	c.-33+14614T>C		intron	N/A	ENSP00000397212.2	Q8NFX7-1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73426 AN: 151858 Hom.: 19524 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.484 AC: 73522 AN: 151976 Hom.: 19562 Cov.: 31 AF XY: 0.482 AC XY: 35815 AN XY: 74266

African (AFR) AF: 0.723 AC: 29952 AN: 41448

American (AMR) AF: 0.402 AC: 6141 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2304 AN: 5144

South Asian (SAS) AF: 0.476 AC: 2295 AN: 4822

European-Finnish (FIN) AF: 0.407 AC: 4295 AN: 10564

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26077 AN: 67944

Other (OTH) AF: 0.451 AC: 950 AN: 2108

Alfa AF: 0.415 Hom.: 42667

Bravo AF: 0.490

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.082
DANN	Benign	0.68
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10147992; hg19: chr14-25503799;