ENST00000514445.5:c.402-575C>A

Variant names:

• chr4-15735478-C-A
• rs11724635
• ENST00000514445.5:c.402-575C>A

Variant summary

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

The ENST00000514445.5(BST1):​c.402-575C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,082 control chromosomes in the GnomAD database, including 16,661 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 (16661 hom., cov: 32)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 84 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 (SAS) allele frequency at 95% confidence interval = 0.563 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

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
	BST1	ENST00000514445.5	TSL:3	c.402-575C>A		intron	N/A	ENSP00000420925.1	H0Y8G4
	BST1	ENST00000514989.1	TSL:3	c.273-2309C>A		intron	N/A	ENSP00000424761.1	H0Y9Q9
	ENSG00000294363	ENST00000723151.1		n.187-1164G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66073 AN: 151964 Hom.: 16658 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.435 AC: 66086 AN: 152082 Hom.: 16661 Cov.: 32 AF XY: 0.440 AC XY: 32687 AN XY: 74308

African (AFR) AF: 0.169 AC: 6997 AN: 41492

American (AMR) AF: 0.504 AC: 7697 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1872 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1941 AN: 5176

South Asian (SAS) AF: 0.581 AC: 2802 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6087 AN: 10550

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37047 AN: 67976

Other (OTH) AF: 0.471 AC: 991 AN: 2106

Alfa AF: 0.446 Hom.: 9951

Bravo AF: 0.414

Asia WGS AF: 0.478 AC: 1662 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	3.0
DANN	Benign	0.23
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11724635;

hg19: chr4-15737101;