4-15740506-C-T

Variant names:

• chr4-15740506-C-T
• rs3893377
• XM_011513878.4:c.851+17572C>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+17572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,976 control chromosomes in the GnomAD database, including 3,107 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 0.20 (3107 hom., cov: 31)
• Consequence: BST1 ENST00000850863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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.187-6192G>A		intron	N/A
	BST1	ENST00000850863.1		n.851+17572C>T		intron	N/A	ENSP00000520950.1	A0ABJ7H2Z9

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29903 AN: 151858 Hom.: 3106 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.197 AC: 29913 AN: 151976 Hom.: 3107 Cov.: 31 AF XY: 0.196 AC XY: 14554 AN XY: 74272

African (AFR) AF: 0.176 AC: 7290 AN: 41440

American (AMR) AF: 0.199 AC: 3044 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1962 AN: 5142

South Asian (SAS) AF: 0.156 AC: 752 AN: 4812

European-Finnish (FIN) AF: 0.177 AC: 1865 AN: 10554

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13427 AN: 67968

Other (OTH) AF: 0.211 AC: 445 AN: 2108

Alfa AF: 0.178 Hom.: 381

Bravo AF: 0.200

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.61
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3893377; hg19: chr4-15742129;