4-15740506-C-T

Variant names:

• chr4-15740506-C-T
• rs3893377
• ENST00000723151.1:n.187-6192G>A

Variant summary

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

The ENST00000723151.1(ENSG00000294363):​n.187-6192G>A 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: ENSG00000294363 ENST00000723151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

Genes affected

ENSG00000294363 (HGNC:58739):

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	XM_011513878.4	c.851+17572C>T		intron_variant	Intron 8 of 8		XP_011512180.1
BST1	XM_017008566.3	c.851+17572C>T		intron_variant	Intron 8 of 8		XP_016864055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294363	ENST00000723151.1	n.187-6192G>A		intron_variant	Intron 2 of 2
BST1	ENST00000850863.1	n.851+17572C>T		intron_variant	Intron 8 of 9			ENSP00000520950.1

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 v4.3

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;