rs4538475

Variant names:

• chr4-15736314-A-C
• rs4538475
• ENST00000514445.5:c.*12+183A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-15736314-A-C
• chr4-15736314-A-G
• chr4-15736314-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000514445.5(BST1):​c.*12+183A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	XM_017008565.3	c.*12+183A>C		intron_variant	Intron 9 of 9		XP_016864054.1
BST1	XM_011513878.4	c.851+13380A>C		intron_variant	Intron 8 of 8		XP_011512180.1
BST1	XM_017008566.3	c.851+13380A>C		intron_variant	Intron 8 of 8		XP_016864055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000514445.5	c.*12+183A>C		intron_variant	Intron 6 of 6	3		ENSP00000420925.1
BST1	ENST00000514989.1	c.273-1473A>C		intron_variant	Intron 4 of 4	3		ENSP00000424761.1
ENSG00000294363	ENST00000723151.1	n.187-2000T>G		intron_variant	Intron 2 of 2
BST1	ENST00000850863.1	n.851+13380A>C		intron_variant	Intron 8 of 9			ENSP00000520950.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs4538475; hg19: chr4-15737937;