chr19-17403506-T-C

Position:

• chr19-17403506-T-C

Variant summary

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

The NM_004335.4(BST2):​c.*15+174A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.96 (67567 hom., cov: 19)
• Consequence: BST2 NM_004335.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

BST2 (HGNC:1119): (bone marrow stromal cell antigen 2) Bone marrow stromal cells are involved in the growth and development of B-cells. The specific function of the protein encoded by the bone marrow stromal cell antigen 2 is undetermined; however, this protein may play a role in pre-B-cell growth and in rheumatoid arthritis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BST2	NM_004335.4	c.*15+174A>G		intron_variant		ENST00000252593.7	NP_004326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BST2	ENST00000252593.7	c.*15+174A>G		intron_variant		1	NM_004335.4	ENSP00000252593	P1
BST2	ENST00000527220.2	c.*188+174A>G		intron_variant, NMD_transcript_variant		2		ENSP00000505650
BST2	ENST00000533098.5	n.373+174A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.958 AC: 140383 AN: 146498 Hom.: 67513 Cov.: 19

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.958 AC: 140487 AN: 146596 Hom.: 67567 Cov.: 19 AF XY: 0.953 AC XY: 67829 AN XY: 71206

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.966

Alfa AF: 0.975 Hom.: 3365

Bravo AF: 0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs919266; hg19: chr19-17514315;