rs171511

Variant names:

• chr17-55196549-C-T
• rs171511
• XR_007065289.1:n.1966-2842C>T

Variant summary

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

The XR_007065289.1(STXBP4):​n.1966-2842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,040 control chromosomes in the GnomAD database, including 6,918 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 (6918 hom., cov: 32)
• Consequence: STXBP4 XR_007065289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43235 AN: 151922 Hom.: 6918 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.284 AC: 43249 AN: 152040 Hom.: 6918 Cov.: 32 AF XY: 0.284 AC XY: 21074 AN XY: 74298

African (AFR) AF: 0.153 AC: 6358 AN: 41490

American (AMR) AF: 0.290 AC: 4424 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3468

East Asian (EAS) AF: 0.131 AC: 678 AN: 5174

South Asian (SAS) AF: 0.316 AC: 1522 AN: 4820

European-Finnish (FIN) AF: 0.390 AC: 4113 AN: 10540

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24241 AN: 67976

Other (OTH) AF: 0.288 AC: 606 AN: 2106

Alfa AF: 0.328 Hom.: 4636

Bravo AF: 0.268

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs171511; hg19: chr17-53273910;