17-55133816-C-T

Position:

• chr17-55133816-C-T

Variant summary

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

The NM_178509.6(STXBP4):​c.1490-7494C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,094 control chromosomes in the GnomAD database, including 31,861 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 0.64 (31861 hom., cov: 32)
• Consequence: STXBP4 NM_178509.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

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]

STXBP4 (HGNC:):

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 = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP4	NM_178509.6	c.1490-7494C>T		intron_variant		ENST00000376352.6	NP_848604.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STXBP4	ENST00000376352.6	c.1490-7494C>T		intron_variant		2	NM_178509.6	ENSP00000365530.2
STXBP4	ENST00000434978.6	c.1424-7494C>T		intron_variant		1		ENSP00000391087.2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96993 AN: 151976 Hom.: 31824 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.638 AC: 97093 AN: 152094 Hom.: 31861 Cov.: 32 AF XY: 0.634 AC XY: 47095 AN XY: 74324

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.610

Alfa AF: 0.620 Hom.: 3639

Bravo AF: 0.638

Asia WGS AF: 0.539 AC: 1875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.61

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: rs2529506; hg19: chr17-53211177;