rs6835705

Variant names:

• chr4-15736747-G-A
• rs6835705
• ENST00000514445.5:c.*12+616G>A

Variant summary

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

The ENST00000514445.5(BST1):​c.*12+616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,100 control chromosomes in the GnomAD database, including 1,652 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 0.11 (1652 hom., cov: 31)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	XM_017008565.3	c.*12+616G>A		intron_variant	Intron 9 of 9		XP_016864054.1
BST1	XM_011513878.4	c.851+13813G>A		intron_variant	Intron 8 of 8		XP_011512180.1
BST1	XM_017008566.3	c.851+13813G>A		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+616G>A		intron_variant	Intron 6 of 6	3		ENSP00000420925.1
BST1	ENST00000514989.1	c.273-1040G>A		intron_variant	Intron 4 of 4	3		ENSP00000424761.1
ENSG00000294363	ENST00000723151.1	n.187-2433C>T		intron_variant	Intron 2 of 2
BST1	ENST00000850863.1	n.851+13813G>A		intron_variant	Intron 8 of 9			ENSP00000520950.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16261 AN: 151982 Hom.: 1653 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0526

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.107 AC: 16285 AN: 152100 Hom.: 1652 Cov.: 31 AF XY: 0.113 AC XY: 8391 AN XY: 74350

African (AFR) AF: 0.175 AC: 7280 AN: 41486

American (AMR) AF: 0.122 AC: 1865 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0526 AC: 182 AN: 3462

East Asian (EAS) AF: 0.522 AC: 2699 AN: 5166

South Asian (SAS) AF: 0.175 AC: 844 AN: 4816

European-Finnish (FIN) AF: 0.0834 AC: 881 AN: 10566

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0337 AC: 2290 AN: 68006

Other (OTH) AF: 0.103 AC: 218 AN: 2110

Alfa AF: 0.0600 Hom.: 699

Bravo AF: 0.116

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.084
DANN	Benign	0.58
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs6835705; hg19: chr4-15738370;