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GeneBe

rs6504950

chr17-54979110-G-A

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 151848 control chromosomes in the gnomAD Genomes database, including 6251 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 ( 6251 hom., cov: 32)

Consequence

STXBP4
NM_178509.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Links

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
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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
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
0.14
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;