19-583460-G-A

Variant names:

• chr19-583460-G-A
• rs6758
• NM_001728.4:c.*716G>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.*716G>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 0.149 in 125,536 control chromosomes in the GnomAD database, including 1,388 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 0.15 (1388 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BSG NM_001728.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BSG	NM_001728.4	c.*716G>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.*716G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_001728.4	ENSP00000333769.3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 18689 AN: 125468 Hom.: 1386 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.145

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.149 AC: 18707 AN: 125536 Hom.: 1388 Cov.: 30 AF XY: 0.159 AC XY: 9634 AN XY: 60476

African (AFR) AF: 0.212 AC: 7312 AN: 34418

American (AMR) AF: 0.117 AC: 1349 AN: 11522

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 363 AN: 3100

East Asian (EAS) AF: 0.234 AC: 983 AN: 4196

South Asian (SAS) AF: 0.294 AC: 1180 AN: 4008

European-Finnish (FIN) AF: 0.242 AC: 1869 AN: 7738

Middle Eastern (MID) AF: 0.154 AC: 41 AN: 266

European-Non Finnish (NFE) AF: 0.0911 AC: 5262 AN: 57784

Other (OTH) AF: 0.150 AC: 258 AN: 1720

Alfa AF: 0.0750 Hom.: 206

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.52
PhyloP100		-1.3
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: rs6758; hg19: chr19-583460;