19-579627-C-T

Variant names:

• chr19-579627-C-T
• rs1803202
• ENST00000545507.6:c.-85C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198590.3. 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.543C>T	p.Asp181Asp	synonymous	Exon 3 of 9	NP_001719.2
	BSG	NM_198590.3		c.-85C>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 8	NP_940992.1	P35613-3
	BSG	NM_001322243.2		c.195C>T	p.Asp65Asp	synonymous	Exon 2 of 8	NP_001309172.1	P35613-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BSG	ENST00000545507.6	TSL:1	c.-85C>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 8	ENSP00000473664.1	P35613-3
	BSG	ENST00000333511.9	TSL:1 MANE Select	c.543C>T	p.Asp181Asp	synonymous	Exon 3 of 9	ENSP00000333769.3	P35613-1
	BSG	ENST00000353555.9	TSL:1	c.195C>T	p.Asp65Asp	synonymous	Exon 2 of 8	ENSP00000343809.4	P35613-2

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

GnomAD2 exomes AF: 0.143 AC: 35090 AN: 245942 AF XY: 0.148

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 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

African (AFR) AF: 0.184 AC: 6164 AN: 33446

American (AMR) AF: 0.0917 AC: 4081 AN: 44512

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 3807 AN: 26036

East Asian (EAS) AF: 0.186 AC: 7378 AN: 39682

South Asian (SAS) AF: 0.267 AC: 23000 AN: 86150

European-Finnish (FIN) AF: 0.166 AC: 8635 AN: 51986

Middle Eastern (MID) AF: 0.194 AC: 1113 AN: 5734

European-Non Finnish (NFE) AF: 0.0884 AC: 98279 AN: 1111242

Other (OTH) AF: 0.128 AC: 7725 AN: 60284

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

African (AFR) AF: 0.181 AC: 7539 AN: 41566

American (AMR) AF: 0.0969 AC: 1482 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 498 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4822

European-Finnish (FIN) AF: 0.182 AC: 1934 AN: 10602

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6730 AN: 68006

Other (OTH) AF: 0.138 AC: 291 AN: 2116

Alfa AF: 0.107 Hom.: 3619

Bravo AF: 0.133

Asia WGS AF: 0.242 AC: 842 AN: 3478

EpiCase AF: 0.101

EpiControl AF: 0.105

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	BSG-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.6
DANN	Benign	0.40
PhyloP100		-0.24
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	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: rs1803202; hg19: chr19-579627; COSMIC: COSV61076551; COSMIC: COSV61076551;