chr3-194672479-A-G

Position:

• chr3-194672479-A-G

Variant summary

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

The 3-194672479-A-G 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSG1	ENST00000480853.1			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;