rs3817198

chr11-1887776-T-C

Variant summary

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

The NM_002339.3(LSP1):c.*13+200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,994 control chromosomes in the GnomAD database, including 5,474 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 (5474 hom., cov: 32)
• Consequence: LSP1 NM_002339.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

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 (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LSP1	NM_002339.3	c.*13+200T>C		intron_variant		ENST00000311604.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSP1	ENST00000311604.8	c.*13+200T>C		intron_variant		1	NM_002339.3	P2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38942 AN: 151876 Hom.: 5475 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.256 AC: 38951 AN: 151994 Hom.: 5474 Cov.: 32 AF XY: 0.254 AC XY: 18868 AN XY: 74286

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.269

Alfa AF: 0.306 Hom.: 14120

Bravo AF: 0.246

Asia WGS AF: 0.215 AC: 750 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	0.96
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3817198; hg19: chr11-1909006;