4-15736314-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000514445.5(BST1):c.*12+183A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
BST1
ENST00000514445.5 intron
ENST00000514445.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0530
Publications
46 publications found
Genes affected
BST1 (HGNC:1118): (bone marrow stromal cell antigen 1) Bone marrow stromal cell antigen-1 is a stromal cell line-derived glycosylphosphatidylinositol-anchored molecule that facilitates pre-B-cell growth. The deduced amino acid sequence exhibits 33% similarity with CD38. BST1 expression is enhanced in bone marrow stromal cell lines derived from patients with rheumatoid arthritis. The polyclonal B-cell abnormalities in rheumatoid arthritis may be, at least in part, attributed to BST1 overexpression in the stromal cell population. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BST1 | XM_017008565.3 | c.*12+183A>T | intron_variant | Intron 9 of 9 | XP_016864054.1 | |||
| BST1 | XM_011513878.4 | c.851+13380A>T | intron_variant | Intron 8 of 8 | XP_011512180.1 | |||
| BST1 | XM_017008566.3 | c.851+13380A>T | intron_variant | Intron 8 of 8 | XP_016864055.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BST1 | ENST00000514445.5 | c.*12+183A>T | intron_variant | Intron 6 of 6 | 3 | ENSP00000420925.1 | ||||
| BST1 | ENST00000514989.1 | c.273-1473A>T | intron_variant | Intron 4 of 4 | 3 | ENSP00000424761.1 | ||||
| ENSG00000294363 | ENST00000723151.1 | n.187-2000T>A | intron_variant | Intron 2 of 2 | ||||||
| BST1 | ENST00000850863.1 | n.851+13380A>T | intron_variant | Intron 8 of 9 | ENSP00000520950.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151698Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
0
AN:
151698
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 151698Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74094
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151698
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
74094
African (AFR)
AF:
AC:
0
AN:
41224
American (AMR)
AF:
AC:
0
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5154
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10536
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67950
Other (OTH)
AF:
AC:
0
AN:
2088
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.