rs8259

Positions:

• chr19-582927-T-A
• chr19-582927-T-C

Variant summary

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

The NM_001728.4(BSG):​c.*183T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 315,186 control chromosomes in the GnomAD database, including 25,330 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 0.40 (12821 hom., cov: 34)
  • Exomes 𝑓: 0.37 (12509 hom.)
• Consequence: BSG NM_001728.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

BSG (HGNC:1116): (basigin (Ok blood group)) The protein encoded by this gene, basigin, is a plasma membrane protein that is important in spermatogenesis, embryo implantation, neural network formation, and tumor progression. Basigin is also a member of the immunoglobulin superfamily, ubiquitously expressed in various tissues. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]

BSG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BSG	NM_001728.4	c.*183T>A		3_prime_UTR_variant	9/9	ENST00000333511.9	NP_001719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BSG	ENST00000333511.9	c.*183T>A		3_prime_UTR_variant	9/9	1	NM_001728.4	ENSP00000333769.3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60230 AN: 151986 Hom.: 12792 Cov.: 34

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.386

GnomAD4 exome AF: 0.365 AC: 59565 AN: 163082 Hom.: 12509 Cov.: 0 AF XY: 0.380 AC XY: 32314 AN XY: 85130

Gnomad4 AFR exome AF: 0.485

Gnomad4 AMR exome AF: 0.369

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.653

Gnomad4 SAS exome AF: 0.592

Gnomad4 FIN exome AF: 0.296

Gnomad4 NFE exome AF: 0.299

Gnomad4 OTH exome AF: 0.359

GnomAD4 genome AF: 0.396 AC: 60286 AN: 152104 Hom.: 12821 Cov.: 34 AF XY: 0.402 AC XY: 29901 AN XY: 74346

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.390

Alfa AF: 0.342 Hom.: 1364

Bravo AF: 0.401

Asia WGS AF: 0.609 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs8259; hg19: chr19-582927; COSMIC: COSV61077072; COSMIC: COSV61077072;