chr14-24858530-A-G

Position:

• chr14-24858530-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394410.1(STXBP6):​c.155-1373T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,160 control chromosomes in the GnomAD database, including 62,772 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 0.90 (62772 hom., cov: 32)
• Consequence: STXBP6 NM_001394410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STXBP6	NM_001394410.1	c.155-1373T>C		intron_variant		ENST00000323944.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STXBP6	ENST00000323944.10	c.155-1373T>C		intron_variant		1	NM_001394410.1	P1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136987 AN: 152042 Hom.: 62737 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.901 AC: 137078 AN: 152160 Hom.: 62772 Cov.: 32 AF XY: 0.904 AC XY: 67233 AN XY: 74408

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.929

Alfa AF: 0.931 Hom.: 8281

Bravo AF: 0.891

Asia WGS AF: 0.975 AC: 3393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs854330; hg19: chr14-25327736;