rs955411

Variant names:

• chr4-15734884-C-T
• rs955411
• ENST00000514445.5:c.402-1169C>T

Variant summary

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

The ENST00000514445.5(BST1):​c.402-1169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,128 control chromosomes in the GnomAD database, including 1,373 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 0.13 (1373 hom., cov: 32)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 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.402-1169C>T		intron	N/A	ENSP00000420925.1	H0Y8G4
	BST1	ENST00000514989.1	TSL:3	c.273-2903C>T		intron	N/A	ENSP00000424761.1	H0Y9Q9
	ENSG00000294363	ENST00000723151.1		n.187-570G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19750 AN: 152010 Hom.: 1371 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19770 AN: 152128 Hom.: 1373 Cov.: 32 AF XY: 0.129 AC XY: 9559 AN XY: 74358

African (AFR) AF: 0.144 AC: 5958 AN: 41478

American (AMR) AF: 0.133 AC: 2030 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0380 AC: 197 AN: 5180

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1487 AN: 10578

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9131 AN: 68006

Other (OTH) AF: 0.127 AC: 267 AN: 2104

Alfa AF: 0.132 Hom.: 2632

Bravo AF: 0.133

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.54
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs955411; hg19: chr4-15736507;