chr9-127612242-GCTCGCGCCGCGCC-G

Variant names:

• chr9-127612242-GCTCGCGCCGCGCC-G
• ENST00000637953:c.-160_-148delTCGCGCCGCGCCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001374309.2(STXBP1):​c.-6+197_-6+209delTCGCGCCGCGCCC variant causes a intron change. The variant allele was found at a frequency of 0.00000226 in 441,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: STXBP1 NM_001374309.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.91

Genes affected

STXBP1 (HGNC:11444): (syntaxin binding protein 1) This gene encodes a syntaxin-binding protein. The encoded protein appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Mutations in this gene have been associated with infantile epileptic encephalopathy-4. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP1	NM_003165.6	c.-161_-149delCTCGCGCCGCGCC		upstream_gene_variant		ENST00000373302.8	NP_003156.1
STXBP1	NM_001032221.6	c.-161_-149delCTCGCGCCGCGCC		upstream_gene_variant		ENST00000373299.5	NP_001027392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP1	ENST00000373302.8	c.-161_-149delCTCGCGCCGCGCC		upstream_gene_variant		1	NM_003165.6	ENSP00000362399.3
STXBP1	ENST00000373299.5	c.-161_-149delCTCGCGCCGCGCC		upstream_gene_variant		1	NM_001032221.6	ENSP00000362396.2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000226 AC: 1 AN: 441642 Hom.: 0 AF XY: 0.00000447 AC XY: 1 AN XY: 223808

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000277

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-130374521;