14-24891169-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.155-34012A>G		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.155-34012A>G		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5

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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.354

Alfa AF: 0.371 Hom.: 1521

Bravo AF: 0.368

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs1241620; hg19: chr14-25360375;