4-15748080-C-T

Position:

• chr4-15748080-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011513878.4(BST1):​c.851+25146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,098 control chromosomes in the GnomAD database, including 5,014 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 (5014 hom., cov: 32)
• Consequence: BST1 XM_011513878.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BST1	XM_011513878.4	c.851+25146C>T		intron_variant			XP_011512180.1
BST1	XM_017008566.3	c.852-11064C>T		intron_variant			XP_016864055.1
		n.15748080C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36984 AN: 151980 Hom.: 5006 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.243 AC: 37017 AN: 152098 Hom.: 5014 Cov.: 32 AF XY: 0.242 AC XY: 18019 AN XY: 74352

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.262

Alfa AF: 0.197 Hom.: 1597

Bravo AF: 0.255

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516292; hg19: chr4-15749703;