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GeneBe

rs6504950

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178509.6(STXBP4):c.-156-6504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,966 control chromosomes in the GnomAD database, including 6,249 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 0.28 ( 6249 hom., cov: 32)

Consequence

STXBP4
NM_178509.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09
Variant links:
Genes affected
STXBP4 (HGNC:19694): (syntaxin binding protein 4) Enables syntaxin binding activity. Involved in several processes, including positive regulation of cell cycle G1/S phase transition; positive regulation of keratinocyte proliferation; and protein stabilization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STXBP4NM_178509.6 linkuse as main transcriptc.-156-6504G>A intron_variant ENST00000376352.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STXBP4ENST00000376352.6 linkuse as main transcriptc.-156-6504G>A intron_variant 2 NM_178509.6 P1Q6ZWJ1-1

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42668
AN:
151848
Hom.:
6251
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.352
Gnomad AMI
AF:
0.135
Gnomad AMR
AF:
0.230
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.0930
Gnomad SAS
AF:
0.169
Gnomad FIN
AF:
0.275
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.276
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42681
AN:
151966
Hom.:
6249
Cov.:
32
AF XY:
0.278
AC XY:
20615
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.352
Gnomad4 AMR
AF:
0.230
Gnomad4 ASJ
AF:
0.233
Gnomad4 EAS
AF:
0.0924
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.275
Gnomad4 NFE
AF:
0.276
Gnomad4 OTH
AF:
0.292
Alfa
AF:
0.279
Hom.:
1412
Bravo
AF:
0.282
Asia WGS
AF:
0.152
AC:
530
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
0.10
Dann
Benign
0.45

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6504950; hg19: chr17-53056471; API