rs907611

Positions:

• chr11-1852842-G-A

Variant summary

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

The ENST00000676039.1(LSP1):​c.-192-111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 505,192 control chromosomes in the GnomAD database, including 21,522 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 0.26 (5707 hom., cov: 33)
  • Exomes 𝑓: 0.29 (15815 hom.)
• Consequence: LSP1 ENST00000676039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

Genes affected

LSP1 (HGNC:6707): (lymphocyte specific protein 1) This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 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
LSP1	ENST00000676039.1	c.-192-111G>A		intron_variant				ENSP00000502383.1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39496 AN: 151822 Hom.: 5707 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.289 AC: 101924 AN: 353268 Hom.: 15815 AF XY: 0.282 AC XY: 52703 AN XY: 187028

Gnomad4 AFR exome AF: 0.119

Gnomad4 AMR exome AF: 0.355

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.237

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.308

Gnomad4 NFE exome AF: 0.316

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.260 AC: 39530 AN: 151924 Hom.: 5707 Cov.: 33 AF XY: 0.259 AC XY: 19244 AN XY: 74240

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.267

Alfa AF: 0.304 Hom.: 9044

Bravo AF: 0.259

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907611; hg19: chr11-1874072;