17-55196549-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP4	XR_007065289.1	n.1966-2842C>T		intron_variant	Intron 18 of 22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;