rs955411

chr4-15734884-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BST1	XM_005248186.3	c.852-2903C>T		intron_variant
BST1	XM_011513878.4	c.851+11950C>T		intron_variant
BST1	XM_011513879.3	c.852-2824C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST1	ENST00000514445.5	c.402-1169C>T		intron_variant		3
BST1	ENST00000514989.1	c.275-2903C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.127

Alfa AF: 0.129 Hom.: 685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955411; hg19: chr4-15736507;