chr19-582927-T-A

Variant names:

• chr19-582927-T-A
• rs8259
• NM_001728.4:c.*183T>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.*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
• Publications: 37 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001728.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BSG	NM_001728.4	MANE Select	c.*183T>A		3_prime_UTR	Exon 9 of 9	NP_001719.2
	BSG	NM_001322243.2		c.*179T>A		3_prime_UTR	Exon 8 of 8	NP_001309172.1	P35613-2
	BSG	NM_198589.3		c.*183T>A		3_prime_UTR	Exon 8 of 8	NP_940991.1	P35613-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BSG	ENST00000333511.9	TSL:1 MANE Select	c.*183T>A		3_prime_UTR	Exon 9 of 9	ENSP00000333769.3	P35613-1
	BSG	ENST00000353555.9	TSL:1	c.*183T>A		3_prime_UTR	Exon 8 of 8	ENSP00000343809.4	P35613-2
	BSG	ENST00000346916.9	TSL:1	c.*183T>A		3_prime_UTR	Exon 7 of 7	ENSP00000344707.4	P35613-3

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

African (AFR) AF: 0.485 AC: 2220 AN: 4582

American (AMR) AF: 0.369 AC: 2143 AN: 5800

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1823 AN: 5158

East Asian (EAS) AF: 0.653 AC: 6284 AN: 9616

South Asian (SAS) AF: 0.592 AC: 10279 AN: 17364

European-Finnish (FIN) AF: 0.296 AC: 2396 AN: 8104

Middle Eastern (MID) AF: 0.372 AC: 868 AN: 2332

European-Non Finnish (NFE) AF: 0.299 AC: 30064 AN: 100422

Other (OTH) AF: 0.359 AC: 3488 AN: 9704

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

African (AFR) AF: 0.496 AC: 20579 AN: 41476

American (AMR) AF: 0.379 AC: 5795 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3466

East Asian (EAS) AF: 0.673 AC: 3469 AN: 5152

South Asian (SAS) AF: 0.601 AC: 2901 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3417 AN: 10590

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21570 AN: 67976

Other (OTH) AF: 0.390 AC: 825 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.84
PhyloP100		-0.16
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8259; hg19: chr19-582927; COSMIC: COSV61077072; COSMIC: COSV61077072;