rs907611

Variant names:

• chr11-1852842-G-A
• rs907611
• ENST00000861224.1:c.-39-264G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000861224.1(LSP1):​c.-39-264G>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 ENST00000861224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 90 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000861224.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSP1	NM_002339.3	MANE Select	c.-303G>A		upstream_gene	N/A	NP_002330.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSP1	ENST00000861224.1		c.-39-264G>A		intron	N/A	ENSP00000531283.1
	LSP1	ENST00000676039.1		c.-192-111G>A		intron	N/A	ENSP00000502383.1
	LSP1	ENST00000311604.8	TSL:1 MANE Select	c.-303G>A		upstream_gene	N/A	ENSP00000308383.4

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

African (AFR) AF: 0.119 AC: 1109 AN: 9330

American (AMR) AF: 0.355 AC: 4517 AN: 12736

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 2411 AN: 10534

East Asian (EAS) AF: 0.237 AC: 5188 AN: 21896

South Asian (SAS) AF: 0.198 AC: 8165 AN: 41142

European-Finnish (FIN) AF: 0.308 AC: 7335 AN: 23828

Middle Eastern (MID) AF: 0.257 AC: 385 AN: 1496

European-Non Finnish (NFE) AF: 0.316 AC: 67172 AN: 212322

Other (OTH) AF: 0.282 AC: 5642 AN: 19984

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

African (AFR) AF: 0.131 AC: 5450 AN: 41470

American (AMR) AF: 0.331 AC: 5059 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 793 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1260 AN: 5162

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3273 AN: 10492

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.319 AC: 21661 AN: 67916

Other (OTH) AF: 0.267 AC: 562 AN: 2108

Alfa AF: 0.303 Hom.: 14533

Bravo AF: 0.259

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.90
PhyloP100		-0.47
PromoterAI		-0.33	Neutral

Splicing

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

Other links and lift over

dbSNP: rs907611; hg19: chr11-1874072;