rs6835705

Positions:

• chr4-15736747-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BST1	XM_005248186.3	c.852-1040G>A		intron_variant
BST1	XM_011513878.4	c.851+13813G>A		intron_variant
BST1	XM_011513879.3	c.852-961G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST1	ENST00000514445.5	c.*12+616G>A		intron_variant		3
BST1	ENST00000514989.1	c.275-1040G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0526

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.0337

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0549 Hom.: 463

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6835705; hg19: chr4-15738370;