rs1803535

Variant names:

• chr19-580710-G-A
• rs1803535
• NM_001728.4:c.720G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-580710-G-A
• chr19-580710-G-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BS1 BS2

The NM_001728.4(BSG):​c.720G>A​(p.Leu240Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 1,592,250 control chromosomes in the GnomAD database, including 847 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.023 (62 hom., cov: 33)
  • Exomes 𝑓: 0.024 (785 hom.)
• Consequence: BSG NM_001728.4 synonymous
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 3.04
• Publications: 6 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 19-580710-G-A is Benign according to our data. Variant chr19-580710-G-A is described in ClinVar as Benign. ClinVar VariationId is 3037529.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=3.04 with no splicing effect.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0232 (3521/152068) while in subpopulation NFE AF = 0.0366 (2481/67856). AF 95% confidence interval is 0.0354. There are 62 homozygotes in GnomAd4. There are 1654 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 62 BG gene

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.720G>A	p.Leu240Leu	synonymous	Exon 5 of 9	NP_001719.2
	BSG	NM_001322243.2		c.372G>A	p.Leu124Leu	synonymous	Exon 4 of 8	NP_001309172.1	P35613-2
	BSG	NM_198589.3		c.372G>A	p.Leu124Leu	synonymous	Exon 4 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.720G>A	p.Leu240Leu	synonymous	Exon 5 of 9	ENSP00000333769.3	P35613-1
	BSG	ENST00000353555.9	TSL:1	c.372G>A	p.Leu124Leu	synonymous	Exon 4 of 8	ENSP00000343809.4	P35613-2
	BSG	ENST00000346916.9	TSL:1	c.93G>A	p.Leu31Leu	synonymous	Exon 3 of 7	ENSP00000344707.4	P35613-3

Frequencies

GnomAD3 genomes AF: 0.0232 AC: 3521 AN: 151950 Hom.: 62 Cov.: 33

Gnomad AFR AF: 0.00572

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00953

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0258

GnomAD2 exomes AF: 0.0241 AC: 6034 AN: 250106 AF XY: 0.0249

Gnomad AFR exome AF: 0.00415

Gnomad AMR exome AF: 0.0161

Gnomad ASJ exome AF: 0.0234

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0202

Gnomad NFE exome AF: 0.0376

Gnomad OTH exome AF: 0.0293

GnomAD4 exome AF: 0.0243 AC: 34955 AN: 1440182 Hom.: 785 Cov.: 52 AF XY: 0.0240 AC XY: 17221 AN XY: 716816

African (AFR) AF: 0.00437 AC: 146 AN: 33406

American (AMR) AF: 0.0135 AC: 596 AN: 44282

Ashkenazi Jewish (ASJ) AF: 0.0201 AC: 519 AN: 25866

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00786 AC: 675 AN: 85868

European-Finnish (FIN) AF: 0.0197 AC: 1023 AN: 52046

Middle Eastern (MID) AF: 0.0325 AC: 186 AN: 5726

European-Non Finnish (NFE) AF: 0.0279 AC: 30531 AN: 1093582

Other (OTH) AF: 0.0214 AC: 1279 AN: 59706

GnomAD4 genome AF: 0.0232 AC: 3521 AN: 152068 Hom.: 62 Cov.: 33 AF XY: 0.0223 AC XY: 1654 AN XY: 74336

African (AFR) AF: 0.00570 AC: 237 AN: 41570

American (AMR) AF: 0.0255 AC: 389 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00954 AC: 46 AN: 4822

European-Finnish (FIN) AF: 0.0185 AC: 196 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2481 AN: 67856

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0319 Hom.: 72

Bravo AF: 0.0236

Asia WGS AF: 0.00404 AC: 14 AN: 3476

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	-0.80
CADD	Benign	2.4
DANN	Benign	0.73
PhyloP100		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1803535; hg19: chr19-580710;