9-99961410-C-T

Position:

• chr9-99961410-C-T

Variant summary

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

The NM_017919.3(STX17):​c.582+1255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,014 control chromosomes in the GnomAD database, including 36,204 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 0.69 (36204 hom., cov: 31)
• Consequence: STX17 NM_017919.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

STX17 (HGNC:11432): (syntaxin 17) Enables SNAP receptor activity; SNARE binding activity; and protein phosphatase binding activity. Involved in several processes, including autophagosome membrane docking; endoplasmic reticulum to Golgi vesicle-mediated transport; and endoplasmic reticulum-Golgi intermediate compartment organization. Acts upstream of or within protein localization to phagophore assembly site. Located in several cellular components, including autophagosome membrane; endoplasmic reticulum-Golgi intermediate compartment; and mitochondria-associated endoplasmic reticulum membrane. Part of SNARE complex. Colocalizes with HOPS complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX17	NM_017919.3	c.582+1255C>T		intron_variant		ENST00000259400.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX17	ENST00000259400.11	c.582+1255C>T		intron_variant		1	NM_017919.3	P1

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104430 AN: 151896 Hom.: 36175 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.688 AC: 104510 AN: 152014 Hom.: 36204 Cov.: 31 AF XY: 0.688 AC XY: 51136 AN XY: 74310

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.655

Alfa AF: 0.673 Hom.: 73142

Bravo AF: 0.681

Asia WGS AF: 0.638 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.24

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: rs10760706; hg19: chr9-102723692;