chr4-15736314-A-G

Variant names:

• chr4-15736314-A-G
• rs4538475
• ENST00000514445.5:c.*12+183A>G

Variant summary

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

The ENST00000514445.5(BST1):​c.*12+183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,716 control chromosomes in the GnomAD database, including 4,905 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 0.24 (4905 hom., cov: 30)
• Consequence: BST1 ENST00000514445.5 intron
• 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]

ENSG00000294363 (HGNC:58739):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514445.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST1	ENST00000514445.5	TSL:3	c.*12+183A>G		intron	N/A	ENSP00000420925.1
	BST1	ENST00000514989.1	TSL:3	c.273-1473A>G		intron	N/A	ENSP00000424761.1
	ENSG00000294363	ENST00000723151.1		n.187-2000T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35964 AN: 151598 Hom.: 4901 Cov.: 30

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.237 AC: 36009 AN: 151716 Hom.: 4905 Cov.: 30 AF XY: 0.242 AC XY: 17928 AN XY: 74168

African (AFR) AF: 0.322 AC: 13294 AN: 41296

American (AMR) AF: 0.254 AC: 3867 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2890 AN: 5140

South Asian (SAS) AF: 0.223 AC: 1071 AN: 4808

European-Finnish (FIN) AF: 0.221 AC: 2328 AN: 10530

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11402 AN: 67924

Other (OTH) AF: 0.231 AC: 486 AN: 2108

Alfa AF: 0.195 Hom.: 13988

Bravo AF: 0.250

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.053

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4538475; hg19: chr4-15737937;