chr19-580388-C-G

Variant names:

• chr19-580388-C-G
• rs2229664
• NM_001728.4:c.582C>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_001728.4(BSG):​c.582C>G​(p.Ser194Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,610,302 control chromosomes in the GnomAD database, including 12,562 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 (1696 hom., cov: 32)
  • Exomes 𝑓: 0.11 (10866 hom.)
• Consequence: BSG NM_001728.4 synonymous
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -5.14

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 19-580388-C-G is Benign according to our data. Variant chr19-580388-C-G is described in ClinVar as [Benign]. Clinvar id is 3059477.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=-5.14 with no splicing effect.
• 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.582C>G	p.Ser194Ser	synonymous_variant	Exon 4 of 9	ENST00000333511.9	NP_001719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSG	ENST00000333511.9	c.582C>G	p.Ser194Ser	synonymous_variant	Exon 4 of 9	1	NM_001728.4	ENSP00000333769.3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21089 AN: 151976 Hom.: 1693 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0968

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: 0.0991

Gnomad OTH AF: 0.134

GnomAD3 exomes AF: 0.141 AC: 34958 AN: 247740 Hom.: 3088 AF XY: 0.147 AC XY: 19711 AN XY: 134540

Gnomad AFR exome AF: 0.186

Gnomad AMR exome AF: 0.0917

Gnomad ASJ exome AF: 0.148

Gnomad EAS exome AF: 0.229

Gnomad SAS exome AF: 0.269

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.0959

Gnomad OTH exome AF: 0.128

GnomAD4 exome AF: 0.110 AC: 159823 AN: 1458208 Hom.: 10866 Cov.: 34 AF XY: 0.115 AC XY: 83247 AN XY: 725454

Gnomad4 AFR exome AF: 0.185

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: 0.162

Gnomad4 NFE exome AF: 0.0884

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.139 AC: 21110 AN: 152094 Hom.: 1696 Cov.: 32 AF XY: 0.145 AC XY: 10763 AN XY: 74336

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0800 Hom.: 204

Bravo AF: 0.133

Asia WGS AF: 0.244 AC: 847 AN: 3476

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	-0.85
CADD	Benign	0.11
DANN	Benign	0.38

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: rs2229664; hg19: chr19-580388; COSMIC: COSV61076436; COSMIC: COSV61076436;