NM_001394410.1:c.154+10014_154+10017dupCACA

Variant names:

• chr14-24964647-C-CTGTG
• rs34132743
• NM_001394410.1:c.154+10014_154+10017dupCACA

Variant summary

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

The NM_001394410.1(STXBP6):​c.154+10014_154+10017dupCACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0069 (7 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 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394410.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	NM_001394410.1	MANE Select	c.154+10014_154+10017dupCACA		intron	N/A	NP_001381339.1	Q8NFX7-1
	STXBP6	NM_001304476.3		c.154+10014_154+10017dupCACA		intron	N/A	NP_001291405.1	Q8NFX7-1
	STXBP6	NM_001304477.3		c.154+10014_154+10017dupCACA		intron	N/A	NP_001291406.1	Q8NFX7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STXBP6	ENST00000323944.10	TSL:1 MANE Select	c.154+10017_154+10018insCACA		intron	N/A	ENSP00000324302.5	Q8NFX7-1
	STXBP6	ENST00000396700.5	TSL:1	c.154+10017_154+10018insCACA		intron	N/A	ENSP00000379928.1	Q8NFX7-1
	STXBP6	ENST00000419632.6	TSL:1	c.154+10017_154+10018insCACA		intron	N/A	ENSP00000397212.2	Q8NFX7-1

Frequencies

GnomAD3 genomes AF: 0.00687 AC: 962 AN: 140110 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00697

Gnomad ASJ AF: 0.00869

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.00243

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.00338

Gnomad NFE AF: 0.00311

Gnomad OTH AF: 0.00685

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

GnomAD4 genome AF: 0.00688 AC: 965 AN: 140194 Hom.: 7 Cov.: 0 AF XY: 0.00750 AC XY: 507 AN XY: 67622

African (AFR) AF: 0.0118 AC: 440 AN: 37288

American (AMR) AF: 0.00696 AC: 97 AN: 13936

Ashkenazi Jewish (ASJ) AF: 0.00869 AC: 29 AN: 3336

East Asian (EAS) AF: 0.0124 AC: 59 AN: 4774

South Asian (SAS) AF: 0.00269 AC: 11 AN: 4094

European-Finnish (FIN) AF: 0.0127 AC: 114 AN: 8986

Middle Eastern (MID) AF: 0.00368 AC: 1 AN: 272

European-Non Finnish (NFE) AF: 0.00311 AC: 201 AN: 64710

Other (OTH) AF: 0.00681 AC: 13 AN: 1908

Alfa AF: 0.00 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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;