19-583460-G-C

Position:

• chr19-583460-G-C

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BSG	NM_001728.4	c.*716G>C		3_prime_UTR_variant	9/9	ENST00000333511.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BSG	ENST00000333511.9	c.*716G>C		3_prime_UTR_variant	9/9	1	NM_001728.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 65 AN: 123950 Hom.: 0 Cov.: 30 FAILED QC

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

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.000440

Gnomad4 AMR AF: 0.000705

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000726

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00146

Gnomad4 NFE AF: 0.000472

Gnomad4 OTH AF: 0.000590

Alfa AF: 0.0000639 Hom.: 147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs6758; hg19: chr19-583460;