14-24964647-CTGTGTGTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant names:

• chr14-24964647-C-CTGTGTGTGTGTGTGTGTGTG
• rs34132743
• NM_001394410.1:c.154+9998_154+10017dupCACACACACACACACACACA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001394410.1(STXBP6):​c.154+9998_154+10017dupCACACACACACACACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0074 (11 hom., cov: 0)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 1 publications found

Genes affected

STXBP6 (HGNC:19666): (syntaxin binding protein 6) Enables cadherin binding activity involved in cell-cell adhesion. Predicted to be involved in Golgi to plasma membrane transport and exocytosis. Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+9998_154+10017dupCACACACACACACACACACA		intron_variant	Intron 2 of 5	ENST00000323944.10	NP_001381339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP6	ENST00000323944.10	c.154+10017_154+10018insCACACACACACACACACACA		intron_variant	Intron 2 of 5	1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.00743 AC: 1041 AN: 140078 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.00974

Gnomad AMI AF: 0.0327

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.00360

Gnomad EAS AF: 0.00146

Gnomad SAS AF: 0.00316

Gnomad FIN AF: 0.00367

Gnomad MID AF: 0.0101

Gnomad NFE AF: 0.00646

Gnomad OTH AF: 0.00843

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

GnomAD4 genome AF: 0.00744 AC: 1043 AN: 140162 Hom.: 11 Cov.: 0 AF XY: 0.00754 AC XY: 510 AN XY: 67604

African (AFR) AF: 0.00977 AC: 364 AN: 37272

American (AMR) AF: 0.0106 AC: 148 AN: 13928

Ashkenazi Jewish (ASJ) AF: 0.00360 AC: 12 AN: 3336

East Asian (EAS) AF: 0.00147 AC: 7 AN: 4774

South Asian (SAS) AF: 0.00318 AC: 13 AN: 4094

European-Finnish (FIN) AF: 0.00367 AC: 33 AN: 8986

Middle Eastern (MID) AF: 0.0110 AC: 3 AN: 272

European-Non Finnish (NFE) AF: 0.00646 AC: 418 AN: 64704

Other (OTH) AF: 0.00839 AC: 16 AN: 1908

Alfa AF: 0.00 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs34132743; hg19: chr14-25433853;