chr14-24964647-C-CTGTGTGTGTG

Position:

• chr14-24964647-C-CTGTGTGTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001394410.1(STXBP6):​c.154+10008_154+10017dupCACACACACA 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 0.025 (65 hom., cov: 0)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0252 (3537/140118) while in subpopulation AFR AF= 0.0472 (1758/37260). AF 95% confidence interval is 0.0453. There are 65 homozygotes in gnomad4. There are 1673 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP6	NM_001394410.1	c.154+10008_154+10017dupCACACACACA		intron_variant		ENST00000323944.10	NP_001381339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STXBP6	ENST00000323944.10	c.154+10008_154+10017dupCACACACACA		intron_variant		1	NM_001394410.1	ENSP00000324302.5

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3525 AN: 140034 Hom.: 65 Cov.: 0

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.00112

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.0230

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0236

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.0216

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

GnomAD4 genome AF: 0.0252 AC: 3537 AN: 140118 Hom.: 65 Cov.: 0 AF XY: 0.0248 AC XY: 1673 AN XY: 67578

Gnomad4 AFR AF: 0.0472

Gnomad4 AMR AF: 0.0154

Gnomad4 ASJ AF: 0.0120

Gnomad4 EAS AF: 0.0229

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0169

Gnomad4 OTH AF: 0.0215

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

LitVar

Other links and lift over

dbSNP: rs34132743; hg19: chr14-25433853;