rs2297060

Variant names:

• chr14-24812013-T-C
• rs2297060
• NM_001394410.1:c.*696A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-24812013-T-C
• chr14-24812013-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394410.1(STXBP6):​c.*696A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,132 control chromosomes in the GnomAD database, including 158 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 0.024 (158 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: STXBP6 NM_001394410.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

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.*696A>G		3_prime_UTR	Exon 6 of 6	NP_001381339.1	Q8NFX7-1
	STXBP6	NM_001304476.3		c.*696A>G		3_prime_UTR	Exon 7 of 7	NP_001291405.1	Q8NFX7-1
	STXBP6	NM_001304477.3		c.*696A>G		3_prime_UTR	Exon 6 of 6	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.*696A>G		3_prime_UTR	Exon 6 of 6	ENSP00000324302.5	Q8NFX7-1
	STXBP6	ENST00000396700.5	TSL:1	c.*696A>G		3_prime_UTR	Exon 7 of 7	ENSP00000379928.1	Q8NFX7-1
	STXBP6	ENST00000886564.1		c.*696A>G		3_prime_UTR	Exon 7 of 7	ENSP00000556623.1

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3569 AN: 152014 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.00353

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0129

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0206

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0236 AC: 3583 AN: 152132 Hom.: 158 Cov.: 32 AF XY: 0.0272 AC XY: 2027 AN XY: 74400

African (AFR) AF: 0.00354 AC: 147 AN: 41518

American (AMR) AF: 0.0132 AC: 202 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.184 AC: 948 AN: 5158

South Asian (SAS) AF: 0.0889 AC: 428 AN: 4816

European-Finnish (FIN) AF: 0.0610 AC: 645 AN: 10582

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1038 AN: 67998

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0143 Hom.: 33

Bravo AF: 0.0195

Asia WGS AF: 0.157 AC: 543 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.74
PhyloP100		0.080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2297060; hg19: chr14-25281219;