19-17403172-T-A

Variant names:

• chr19-17403172-T-A
• rs9576
• NM_004335.4:c.*170A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004335.4(BST2):​c.*170A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BST2 NM_004335.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 8 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004335.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST2	NM_004335.4	MANE Select	c.*170A>T		3_prime_UTR	Exon 5 of 5	NP_004326.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST2	ENST00000252593.7	TSL:1 MANE Select	c.*170A>T		3_prime_UTR	Exon 5 of 5	ENSP00000252593.6
	BST2	ENST00000527220.2	TSL:2	n.*343A>T		non_coding_transcript_exon	Exon 4 of 4	ENSP00000505650.1
	BST2	ENST00000527220.2	TSL:2	n.*343A>T		3_prime_UTR	Exon 4 of 4	ENSP00000505650.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 837418 Hom.: 0 Cov.: 64 AF XY: 0.00 AC XY: 0 AN XY: 387196

African (AFR) AF: 0.00 AC: 0 AN: 15806

American (AMR) AF: 0.00 AC: 0 AN: 1520

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5184

East Asian (EAS) AF: 0.00 AC: 0 AN: 3660

South Asian (SAS) AF: 0.00 AC: 0 AN: 17188

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 354

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1630

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 764612

Other (OTH) AF: 0.00 AC: 0 AN: 27464

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.19
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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

Other links and lift over

dbSNP: rs9576; hg19: chr19-17513981;