rs7978987

chr12-130796949-G-Achr12-130796949-G-T

Variant summary

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

The NM_194356.4(STX2):c.787-829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,082 control chromosomes in the GnomAD database, including 9,430 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 0.35 (9430 hom., cov: 33)
• Consequence: STX2 NM_194356.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

STX2 (HGNC:3403): (syntaxin 2) The product of this gene belongs to the syntaxin/epimorphin family of proteins. The syntaxins are a large protein family implicated in the targeting and fusion of intracellular transport vesicles. The product of this gene regulates epithelial-mesenchymal interactions and epithelial cell morphogenesis and activation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX2	NM_194356.4	c.787-829C>T		intron_variant		ENST00000392373.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX2	ENST00000392373.7	c.787-829C>T		intron_variant		5	NM_194356.4	P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52576 AN: 151964 Hom.: 9413 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.346 AC: 52624 AN: 152082 Hom.: 9430 Cov.: 33 AF XY: 0.342 AC XY: 25422 AN XY: 74306

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.355

Alfa AF: 0.340 Hom.: 1163

Bravo AF: 0.354

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.50

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: rs7978987; hg19: chr12-131281494;