chr14-24891169-T-C

Variant names:

• chr14-24891169-T-C
• rs1241620
• NM_001394410.1:c.155-34012A>G

Variant summary

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

The NM_001394410.1(STXBP6):​c.155-34012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,030 control chromosomes in the GnomAD database, including 10,384 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 0.37 (10384 hom., cov: 32)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 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.155-34012A>G		intron	N/A	NP_001381339.1	Q8NFX7-1
	STXBP6	NM_001304476.3		c.155-34012A>G		intron	N/A	NP_001291405.1	Q8NFX7-1
	STXBP6	NM_001304477.3		c.155-34012A>G		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.155-34012A>G		intron	N/A	ENSP00000324302.5	Q8NFX7-1
	STXBP6	ENST00000396700.5	TSL:1	c.155-34012A>G		intron	N/A	ENSP00000379928.1	Q8NFX7-1
	STXBP6	ENST00000419632.6	TSL:1	c.155-34012A>G		intron	N/A	ENSP00000397212.2	Q8NFX7-1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55515 AN: 151912 Hom.: 10375 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.365 AC: 55564 AN: 152030 Hom.: 10384 Cov.: 32 AF XY: 0.360 AC XY: 26785 AN XY: 74348

African (AFR) AF: 0.408 AC: 16922 AN: 41466

American (AMR) AF: 0.290 AC: 4426 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5162

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3324 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25264 AN: 67944

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.372 Hom.: 1587

Bravo AF: 0.368

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.56
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1241620; hg19: chr14-25360375;