rs1675923

Variant names:

• chr3-194672479-A-G
• rs1675923
• ENST00000480853.1:n.-16T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000480853.1(LSG1):​n.-16T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 277,852 control chromosomes in the GnomAD database, including 14,768 homozygotes. 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 0.29 (6986 hom., cov: 33)
  • Exomes 𝑓: 0.34 (7782 hom.)
• Consequence: LSG1 ENST00000480853.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

LSG1 (HGNC:25652): (large 60S subunit nuclear export GTPase 1) This gene encodes a protein related to the yeast large subunit GTPase 1. The encoded protein is necessary for cell viability and may localize in the endoplasmic reticulum, nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSG1	ENST00000480853.1	n.-16T>C		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43814 AN: 151862 Hom.: 6983 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.338 AC: 42542 AN: 125872 Hom.: 7782 Cov.: 0 AF XY: 0.335 AC XY: 22112 AN XY: 65964

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.265

Gnomad4 ASJ exome AF: 0.327

Gnomad4 EAS exome AF: 0.201

Gnomad4 SAS exome AF: 0.258

Gnomad4 FIN exome AF: 0.342

Gnomad4 NFE exome AF: 0.374

Gnomad4 OTH exome AF: 0.330

GnomAD4 genome AF: 0.288 AC: 43799 AN: 151980 Hom.: 6986 Cov.: 33 AF XY: 0.287 AC XY: 21311 AN XY: 74296

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.322

Alfa AF: 0.307 Hom.: 1353

Bravo AF: 0.278

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1675923; hg19: chr3-194393208;