19-579627-C-T

Variant names:

• chr19-579627-C-T
• rs1803202
• ENST00000545507:c.-85C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_198590.3(BSG):​c.-85C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,611,332 control chromosomes in the GnomAD database, including 12,594 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.14 (1694 hom., cov: 34)
  • Exomes 𝑓: 0.11 (10900 hom.)
• Consequence: BSG NM_198590.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.244

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 19-579627-C-T is Benign according to our data. Variant chr19-579627-C-T is described in ClinVar as [Benign]. Clinvar id is 3059371.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BSG	NM_001728.4	c.543C>T	p.Asp181Asp	synonymous_variant	Exon 3 of 9	ENST00000333511.9	NP_001719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSG	ENST00000333511.9	c.543C>T	p.Asp181Asp	synonymous_variant	Exon 3 of 9	1	NM_001728.4	ENSP00000333769.3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21110 AN: 152142 Hom.: 1692 Cov.: 34

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.134

GnomAD3 exomes AF: 0.143 AC: 35090 AN: 245942 Hom.: 3128 AF XY: 0.148 AC XY: 19773 AN XY: 133792

Gnomad AFR exome AF: 0.186

Gnomad AMR exome AF: 0.0919

Gnomad ASJ exome AF: 0.149

Gnomad EAS exome AF: 0.229

Gnomad SAS exome AF: 0.270

Gnomad FIN exome AF: 0.174

Gnomad NFE exome AF: 0.0965

Gnomad OTH exome AF: 0.129

GnomAD4 exome AF: 0.110 AC: 160182 AN: 1459072 Hom.: 10900 Cov.: 32 AF XY: 0.115 AC XY: 83404 AN XY: 725816

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.0917

Gnomad4 ASJ exome AF: 0.146

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.166

Gnomad4 NFE exome AF: 0.0884

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.139 AC: 21123 AN: 152260 Hom.: 1694 Cov.: 34 AF XY: 0.145 AC XY: 10767 AN XY: 74438

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.138

Alfa AF: 0.105 Hom.: 1387

Bravo AF: 0.133

Asia WGS AF: 0.242 AC: 842 AN: 3478

EpiCase AF: 0.101

EpiControl AF: 0.105

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

BSG-related disorder Benign:1

Oct 31, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.6
DANN	Benign	0.40
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: rs1803202; hg19: chr19-579627; COSMIC: COSV61076551; COSMIC: COSV61076551;