rs3213710

Variant names:

• chr4-15715698-G-A
• rs3213710
• NM_004334.3:c.612-9G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004334.3(BST1):​c.612-9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 1,557,570 control chromosomes in the GnomAD database, including 207,443 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 0.45 (16451 hom., cov: 32)
  • Exomes 𝑓: 0.52 (190992 hom.)
• Consequence: BST1 NM_004334.3 intron
• Scores: Splicing: ADA: 0.001913
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 34 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	NM_004334.3	c.612-9G>A		intron_variant	Intron 5 of 8	ENST00000265016.9	NP_004325.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000265016.9	c.612-9G>A		intron_variant	Intron 5 of 8	1	NM_004334.3	ENSP00000265016.4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67944 AN: 151840 Hom.: 16443 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.473

GnomAD2 exomes AF: 0.518 AC: 118741 AN: 229426 AF XY: 0.523

Gnomad AFR exome AF: 0.247

Gnomad AMR exome AF: 0.628

Gnomad ASJ exome AF: 0.479

Gnomad EAS exome AF: 0.437

Gnomad FIN exome AF: 0.558

Gnomad NFE exome AF: 0.519

Gnomad OTH exome AF: 0.520

GnomAD4 exome AF: 0.518 AC: 727548 AN: 1405612 Hom.: 190992 Cov.: 24 AF XY: 0.520 AC XY: 363982 AN XY: 699828

African (AFR) AF: 0.255 AC: 8018 AN: 31446

American (AMR) AF: 0.614 AC: 23642 AN: 38512

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 12151 AN: 25248

East Asian (EAS) AF: 0.427 AC: 16494 AN: 38624

South Asian (SAS) AF: 0.583 AC: 46295 AN: 79414

European-Finnish (FIN) AF: 0.557 AC: 29462 AN: 52882

Middle Eastern (MID) AF: 0.583 AC: 3268 AN: 5604

European-Non Finnish (NFE) AF: 0.519 AC: 558561 AN: 1075626

Other (OTH) AF: 0.509 AC: 29657 AN: 58256

GnomAD4 genome AF: 0.447 AC: 67969 AN: 151958 Hom.: 16451 Cov.: 32 AF XY: 0.452 AC XY: 33564 AN XY: 74254

African (AFR) AF: 0.259 AC: 10716 AN: 41424

American (AMR) AF: 0.521 AC: 7955 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2229 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2717 AN: 4814

European-Finnish (FIN) AF: 0.561 AC: 5918 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35151 AN: 67952

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.507 Hom.: 42838

Bravo AF: 0.435

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		-0.027
PromoterAI		-0.0074	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0019
dbscSNV1_RF	Benign	0.028
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3213710; hg19: chr4-15717321; COSMIC: COSV53947006;