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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	XM_017008565.3	c.852-1169C>T		intron_variant	Intron 8 of 9		XP_016864054.1
BST1	XM_011513878.4	c.851+11950C>T		intron_variant	Intron 8 of 8		XP_011512180.1
BST1	XM_017008566.3	c.851+11950C>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.402-1169C>T		intron_variant	Intron 5 of 6	3		ENSP00000420925.1
BST1	ENST00000514989.1	c.273-2903C>T		intron_variant	Intron 4 of 4	3		ENSP00000424761.1
ENSG00000294363	ENST00000723151.1	n.187-570G>A		intron_variant	Intron 2 of 2
BST1	ENST00000850863.1	n.851+11950C>T		intron_variant	Intron 8 of 9			ENSP00000520950.1

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 v4.3

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;