rs7978987

Variant names:

• chr12-130796949-G-A
• rs7978987
• NM_194356.4:c.787-829C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-130796949-G-A
• chr12-130796949-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

STX2 Gene-Disease associations (from GenCC):

• spermatogenic failure

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STX2	NM_194356.4	c.787-829C>T		intron_variant	Intron 9 of 10	ENST00000392373.7	NP_919337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX2	ENST00000392373.7	c.787-829C>T		intron_variant	Intron 9 of 10	5	NM_194356.4	ENSP00000376178.2

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

African (AFR) AF: 0.400 AC: 16571 AN: 41472

American (AMR) AF: 0.354 AC: 5413 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.116 AC: 599 AN: 5170

South Asian (SAS) AF: 0.239 AC: 1149 AN: 4816

European-Finnish (FIN) AF: 0.305 AC: 3218 AN: 10562

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22992 AN: 67988

Other (OTH) AF: 0.355 AC: 749 AN: 2108

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
PhyloP100		-0.55
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: rs7978987; hg19: chr12-131281494;