rs6504950

Variant names:

• chr17-54979110-G-A
• rs6504950
• NM_178509.6:c.-156-6504G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178509.6(STXBP4):​c.-156-6504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,966 control chromosomes in the GnomAD database, including 6,249 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 0.28 (6249 hom., cov: 32)
• Consequence: STXBP4 NM_178509.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

STXBP4 (HGNC:19694): (syntaxin binding protein 4) Enables syntaxin binding activity. Involved in several processes, including positive regulation of cell cycle G1/S phase transition; positive regulation of keratinocyte proliferation; and protein stabilization. Located in extracellular exosome. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP4	NM_178509.6	c.-156-6504G>A		intron_variant	Intron 1 of 17	ENST00000376352.6	NP_848604.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP4	ENST00000376352.6	c.-156-6504G>A		intron_variant	Intron 1 of 17	2	NM_178509.6	ENSP00000365530.2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42668 AN: 151848 Hom.: 6251 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.281 AC: 42681 AN: 151966 Hom.: 6249 Cov.: 32 AF XY: 0.278 AC XY: 20615 AN XY: 74284

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.292

Alfa AF: 0.279 Hom.: 1412

Bravo AF: 0.282

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs6504950; hg19: chr17-53056471;