4-15735725-G-A

Variant names:

• chr4-15735725-G-A
• rs4698412
• ENST00000514445.5:c.402-328G>A

Variant summary

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

The ENST00000514445.5(BST1):​c.402-328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,084 control chromosomes in the GnomAD database, including 16,638 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 0.43 (16638 hom., cov: 32)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 70 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514445.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST1	ENST00000514445.5	TSL:3	c.402-328G>A		intron	N/A	ENSP00000420925.1
	BST1	ENST00000514989.1	TSL:3	c.273-2062G>A		intron	N/A	ENSP00000424761.1
	ENSG00000294363	ENST00000723151.1		n.187-1411C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66041 AN: 151966 Hom.: 16635 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.434 AC: 66054 AN: 152084 Hom.: 16638 Cov.: 32 AF XY: 0.440 AC XY: 32673 AN XY: 74316

African (AFR) AF: 0.168 AC: 6990 AN: 41512

American (AMR) AF: 0.504 AC: 7700 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1941 AN: 5152

South Asian (SAS) AF: 0.581 AC: 2805 AN: 4824

European-Finnish (FIN) AF: 0.574 AC: 6058 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37048 AN: 67972

Other (OTH) AF: 0.469 AC: 988 AN: 2108

Alfa AF: 0.506 Hom.: 72837

Bravo AF: 0.414

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4698412; hg19: chr4-15737348;