19-583460-G-C

Variant names:

• chr19-583460-G-C
• rs6758
• NM_001728.4:c.*716G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001728.4(BSG):​c.*716G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.00053 (0 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: 11 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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.*716G>C		3_prime_UTR	Exon 9 of 9	NP_001719.2
	BSG	NM_001322243.2		c.*712G>C		3_prime_UTR	Exon 8 of 8	NP_001309172.1	P35613-2
	BSG	NM_198589.3		c.*716G>C		3_prime_UTR	Exon 8 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.*716G>C		3_prime_UTR	Exon 9 of 9	ENSP00000333769.3	P35613-1
	BSG	ENST00000353555.9	TSL:1	c.*716G>C		3_prime_UTR	Exon 8 of 8	ENSP00000343809.4	P35613-2
	BSG	ENST00000346916.9	TSL:1	c.*716G>C		3_prime_UTR	Exon 7 of 7	ENSP00000344707.4	P35613-3

Frequencies

GnomAD3 genomes AF: 0.000524 AC: 65 AN: 123950 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000412

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000706

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000724

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00146

Gnomad MID AF: 0.00350

Gnomad NFE AF: 0.000472

Gnomad OTH AF: 0.000597

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR 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 Data not reliable, filtered out with message: AS_VQSR AF: 0.000532 AC: 66 AN: 124020 Hom.: 0 Cov.: 30 AF XY: 0.000570 AC XY: 34 AN XY: 59678

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000440 AC: 15 AN: 34074

American (AMR) AF: 0.000705 AC: 8 AN: 11350

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3064

East Asian (EAS) AF: 0.000726 AC: 3 AN: 4134

South Asian (SAS) AF: 0.00 AC: 0 AN: 3956

European-Finnish (FIN) AF: 0.00146 AC: 11 AN: 7540

Middle Eastern (MID) AF: 0.00376 AC: 1 AN: 266

European-Non Finnish (NFE) AF: 0.000472 AC: 27 AN: 57168

Other (OTH) AF: 0.000590 AC: 1 AN: 1694

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0000506 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.18
PhyloP100		-1.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6758;

hg19: chr19-583460;