chr17-55088962-A-G

Variant names:

• chr17-55088962-A-G
• rs10515089
• NM_178509.6:c.1489+7779A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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]

LOC107985002 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STXBP4	NM_178509.6	c.1489+7779A>G		intron_variant	Intron 16 of 17	ENST00000376352.6	NP_848604.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP4	ENST00000376352.6	c.1489+7779A>G		intron_variant	Intron 16 of 17	2	NM_178509.6	ENSP00000365530.2
STXBP4	ENST00000434978.6	c.1423+7779A>G		intron_variant	Intron 15 of 16	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

African (AFR) AF: 0.0962 AC: 3996 AN: 41546

American (AMR) AF: 0.329 AC: 5020 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1802 AN: 5158

South Asian (SAS) AF: 0.147 AC: 707 AN: 4818

European-Finnish (FIN) AF: 0.148 AC: 1568 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11414 AN: 68008

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.177 Hom.: 8553

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
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10515089; hg19: chr17-53166323;