rs1675923

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000294298 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294298	ENST00000722575.1	n.-135A>G		upstream_gene_variant
ENSG00000294298	ENST00000722576.1	n.-129A>G		upstream_gene_variant

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

African (AFR) AF: 0.157 AC: 554 AN: 3526

American (AMR) AF: 0.265 AC: 858 AN: 3234

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1547 AN: 4736

East Asian (EAS) AF: 0.201 AC: 1583 AN: 7862

South Asian (SAS) AF: 0.258 AC: 2739 AN: 10616

European-Finnish (FIN) AF: 0.342 AC: 2447 AN: 7156

Middle Eastern (MID) AF: 0.359 AC: 245 AN: 682

European-Non Finnish (NFE) AF: 0.374 AC: 29894 AN: 79942

Other (OTH) AF: 0.330 AC: 2675 AN: 8118

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

African (AFR) AF: 0.152 AC: 6285 AN: 41484

American (AMR) AF: 0.297 AC: 4540 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4816

European-Finnish (FIN) AF: 0.321 AC: 3385 AN: 10558

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25049 AN: 67904

Other (OTH) AF: 0.322 AC: 679 AN: 2108

Alfa AF: 0.313 Hom.: 2770

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
PhyloP100		2.1
PromoterAI		0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1675923; hg19: chr3-194393208;