rs13676

chr19-583268-G-A

Variant summary

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

The NM_001728.4(BSG):c.*524G>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 0.055 in 152,474 control chromosomes in the GnomAD database, including 372 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 0.055 (372 hom., cov: 33)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: BSG NM_001728.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BSG	NM_001728.4	c.*524G>A		3_prime_UTR_variant	9/9	ENST00000333511.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BSG	ENST00000333511.9	c.*524G>A		3_prime_UTR_variant	9/9	1	NM_001728.4	P1

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8382 AN: 152178 Hom.: 371 Cov.: 33

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.00901

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0626

GnomAD4 exome AF: 0.0562 AC: 10 AN: 178 Hom.: 0 Cov.: 0 AF XY: 0.0328 AC XY: 4 AN XY: 122

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0467

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0550 AC: 8379 AN: 152296 Hom.: 372 Cov.: 33 AF XY: 0.0581 AC XY: 4327 AN XY: 74462

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0589

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0624 Hom.: 380

Bravo AF: 0.0576

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.1
Dann	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs13676; hg19: chr19-583268;