4-15748080-C-T

Variant names:

• chr4-15748080-C-T
• rs10516292
• XM_011513878.4:c.851+25146C>T

Variant summary

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

The ENST00000850863.1(BST1):​n.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 ENST00000850863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850863.1. 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
	ENSG00000294363	ENST00000723151.1		n.186+6379G>A		intron	N/A
	BST1	ENST00000850863.1		n.851+25146C>T		intron	N/A	ENSP00000520950.1	A0ABJ7H2Z9

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

African (AFR) AF: 0.321 AC: 13328 AN: 41488

American (AMR) AF: 0.238 AC: 3636 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2763 AN: 5168

South Asian (SAS) AF: 0.201 AC: 971 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12701 AN: 67988

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.206 Hom.: 2993

Bravo AF: 0.255

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10516292; hg19: chr4-15749703;