rs12646913

Variant names:

• chr4-15737653-A-G
• rs12646913
• ENST00000514445.5:c.*13-134A>G

Variant summary

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

The ENST00000514445.5(BST1):​c.*13-134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 475,442 control chromosomes in the GnomAD database, including 1,860 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 0.098 (910 hom., cov: 32)
  • Exomes 𝑓: 0.071 (950 hom.)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST1	ENST00000514445.5	TSL:3	c.*13-134A>G		intron	N/A	ENSP00000420925.1	H0Y8G4
	BST1	ENST00000514989.1	TSL:3	c.273-134A>G		intron	N/A	ENSP00000424761.1	H0Y9Q9
	ENSG00000294363	ENST00000723151.1		n.187-3339T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14859 AN: 151504 Hom.: 902 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.0707 AC: 22890 AN: 323830 Hom.: 950 AF XY: 0.0699 AC XY: 12441 AN XY: 177948

African (AFR) AF: 0.147 AC: 1116 AN: 7578

American (AMR) AF: 0.0560 AC: 1261 AN: 22504

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 1236 AN: 8316

East Asian (EAS) AF: 0.0561 AC: 502 AN: 8954

South Asian (SAS) AF: 0.0563 AC: 3061 AN: 54410

European-Finnish (FIN) AF: 0.0325 AC: 360 AN: 11072

Middle Eastern (MID) AF: 0.151 AC: 408 AN: 2694

European-Non Finnish (NFE) AF: 0.0706 AC: 13711 AN: 194170

Other (OTH) AF: 0.0874 AC: 1235 AN: 14132

GnomAD4 genome AF: 0.0982 AC: 14894 AN: 151612 Hom.: 910 Cov.: 32 AF XY: 0.0945 AC XY: 7009 AN XY: 74170

African (AFR) AF: 0.157 AC: 6404 AN: 40894

American (AMR) AF: 0.0960 AC: 1466 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3470

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5186

South Asian (SAS) AF: 0.0556 AC: 269 AN: 4834

European-Finnish (FIN) AF: 0.0249 AC: 265 AN: 10624

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0774 AC: 5264 AN: 68024

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.0847 Hom.: 331

Bravo AF: 0.107

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12646913; hg19: chr4-15739276;