4-15748080-C-T

Variant names:

• chr4-15748080-C-T
• rs10516292
• ENST00000723151.1:n.186+6379G>A

Variant summary

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

The ENST00000723151.1(ENSG00000294363):​n.186+6379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,098 control chromosomes in the GnomAD database, including 5,014 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 0.24 (5014 hom., cov: 32)
• Consequence: ENSG00000294363 ENST00000723151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 10 publications found

Genes affected

ENSG00000294363 (HGNC:58739):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	XM_011513878.4	c.851+25146C>T		intron_variant	Intron 8 of 8		XP_011512180.1
BST1	XM_017008566.3	c.852-11064C>T		intron_variant	Intron 8 of 8		XP_016864055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294363	ENST00000723151.1	n.186+6379G>A		intron_variant	Intron 2 of 2
BST1	ENST00000850863.1	n.851+25146C>T		intron_variant	Intron 8 of 9			ENSP00000520950.1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36984 AN: 151980 Hom.: 5006 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.243 AC: 37017 AN: 152098 Hom.: 5014 Cov.: 32 AF XY: 0.242 AC XY: 18019 AN XY: 74352

African (AFR) AF: 0.321 AC: 13328 AN: 41488

American (AMR) AF: 0.238 AC: 3636 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2763 AN: 5168

South Asian (SAS) AF: 0.201 AC: 971 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12701 AN: 67988

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.206 Hom.: 2993

Bravo AF: 0.255

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10516292; hg19: chr4-15749703;