19-17403172-T-G

Variant summary

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

The NM_004335.4(BST2):c.*170A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 989,458 control chromosomes in the GnomAD database, including 447,040 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 0.91 (63820 hom., cov: 30)
  • Exomes 𝑓: 0.96 (383220 hom.)
• Consequence: BST2 NM_004335.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST2	NM_004335.4	c.*170A>C		3_prime_UTR_variant	5/5	ENST00000252593.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST2	ENST00000252593.7	c.*170A>C		3_prime_UTR_variant	5/5	1	NM_004335.4	P1
BST2	ENST00000527220.2	c.*343A>C		3_prime_UTR_variant, NMD_transcript_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138843 AN: 151924 Hom.: 63772 Cov.: 30

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.939

GnomAD4 exome AF: 0.956 AC: 800767 AN: 837414 Hom.: 383220 Cov.: 64 AF XY: 0.957 AC XY: 370488 AN XY: 387194

Gnomad4 AFR exome AF: 0.862

Gnomad4 AMR exome AF: 0.925

Gnomad4 ASJ exome AF: 0.991

Gnomad4 EAS exome AF: 0.602

Gnomad4 SAS exome AF: 0.960

Gnomad4 FIN exome AF: 0.910

Gnomad4 NFE exome AF: 0.960

Gnomad4 OTH exome AF: 0.943

GnomAD4 genome AF: 0.914 AC: 138948 AN: 152044 Hom.: 63820 Cov.: 30 AF XY: 0.909 AC XY: 67566 AN XY: 74300

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.941

Alfa AF: 0.952 Hom.: 132068

Bravo AF: 0.911

Asia WGS AF: 0.822 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.2
Dann	Benign	0.42
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

Publications

LitVar

Other links and lift over

dbSNP: rs9576; hg19: chr19-17513981;