17-55088962-A-G

Position:

• chr17-55088962-A-G

Variant summary

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

The NM_178509.6(STXBP4):​c.1489+7779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,188 control chromosomes in the GnomAD database, including 2,688 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 0.17 (2688 hom., cov: 32)
• Consequence: STXBP4 NM_178509.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

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]

LOC107985002 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP4	NM_178509.6	c.1489+7779A>G		intron_variant		ENST00000376352.6	NP_848604.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STXBP4	ENST00000376352.6	c.1489+7779A>G		intron_variant		2	NM_178509.6	ENSP00000365530.2
STXBP4	ENST00000434978.6	c.1423+7779A>G		intron_variant		1		ENSP00000391087.2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26006 AN: 152070 Hom.: 2688 Cov.: 32

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.171 AC: 26017 AN: 152188 Hom.: 2688 Cov.: 32 AF XY: 0.173 AC XY: 12901 AN XY: 74390

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.190

Alfa AF: 0.180 Hom.: 5483

Bravo AF: 0.186

Asia WGS AF: 0.239 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.81

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: rs10515089; hg19: chr17-53166323;