rs13676

Variant names:

• chr19-583268-G-A
• rs13676
• NM_001728.4:c.*524G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BSG	NM_001728.4	c.*524G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000333511.9	NP_001719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSG	ENST00000333511.9	c.*524G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_001728.4	ENSP00000333769.3

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0467 AC: 7 AN: 150

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.0142 AC: 590 AN: 41570

American (AMR) AF: 0.133 AC: 2037 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3470

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5190

South Asian (SAS) AF: 0.102 AC: 491 AN: 4830

European-Finnish (FIN) AF: 0.0589 AC: 625 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4275 AN: 68020

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0604 Hom.: 591

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
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs13676; hg19: chr19-583268;