rs3817197

chr11-1884944-G-Achr11-1884944-G-C

Variant summary

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

The NM_002339.3(LSP1):c.717+363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,608 control chromosomes in the GnomAD database, including 17,778 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 0.48 (17778 hom., cov: 30)
• Consequence: LSP1 NM_002339.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LSP1	NM_002339.3	c.717+363G>A		intron_variant		ENST00000311604.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSP1	ENST00000311604.8	c.717+363G>A		intron_variant		1	NM_002339.3	P2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72137 AN: 151490 Hom.: 17760 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.476 AC: 72202 AN: 151608 Hom.: 17778 Cov.: 30 AF XY: 0.482 AC XY: 35708 AN XY: 74078

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.488

Alfa AF: 0.479 Hom.: 24340

Bravo AF: 0.484

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.24
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3817197; hg19: chr11-1906174;