11-1884944-G-A

Variant names:

• chr11-1884944-G-A
• rs3817197
• NM_002339.3:c.717+363G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002339.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSP1	NM_002339.3	MANE Select	c.717+363G>A		intron	N/A	NP_002330.1
	LSP1	NM_001242932.2		c.1101+363G>A		intron	N/A	NP_001229861.1
	LSP1	NM_001013253.2		c.531+363G>A		intron	N/A	NP_001013271.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSP1	ENST00000311604.8	TSL:1 MANE Select	c.717+363G>A		intron	N/A	ENSP00000308383.4
	LSP1	ENST00000381775.5	TSL:2	c.1101+363G>A		intron	N/A	ENSP00000371194.1
	LSP1	ENST00000405957.6	TSL:5	c.531+363G>A		intron	N/A	ENSP00000383932.2

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

African (AFR) AF: 0.386 AC: 15931 AN: 41278

American (AMR) AF: 0.599 AC: 9135 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4154 AN: 5142

South Asian (SAS) AF: 0.517 AC: 2489 AN: 4810

European-Finnish (FIN) AF: 0.499 AC: 5235 AN: 10494

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31995 AN: 67870

Other (OTH) AF: 0.488 AC: 1029 AN: 2110

Alfa AF: 0.480 Hom.: 33450

Bravo AF: 0.484

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.42
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3817197; hg19: chr11-1906174;