chr4-15724941-G-A

Position:

• chr4-15724941-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004334.3(BST1):​c.851+2007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 152,210 control chromosomes in the GnomAD database, including 503 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 0.070 (503 hom., cov: 32)
• Consequence: BST1 NM_004334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BST1	NM_004334.3	c.851+2007G>A		intron_variant		ENST00000265016.9	NP_004325.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000265016.9	c.851+2007G>A		intron_variant		1	NM_004334.3	ENSP00000265016	P1
BST1	ENST00000382346.7	c.896+2007G>A		intron_variant		5		ENSP00000371783
BST1	ENST00000514445.5	c.401+2007G>A		intron_variant		3		ENSP00000420925
BST1	ENST00000514989.1	c.274+2007G>A		intron_variant		3		ENSP00000424761

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10588 AN: 152092 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0924

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0696 AC: 10596 AN: 152210 Hom.: 503 Cov.: 32 AF XY: 0.0687 AC XY: 5114 AN XY: 74394

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0902 Hom.: 441

Bravo AF: 0.0660

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12502586; hg19: chr4-15726564;