dbSNP rs907611: LSP1:c.-192-111G>A (chr11-1852842-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Publications

90 publications found

Variant links:

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]

LSP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSP1	NM_002339.3 link	c.-303G>A		upstream_gene_variant		ENST00000311604.8	NP_002330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSP1	ENST00000676039.1 link	c.-192-111G>A		intron_variant	Intron 1 of 1			ENSP00000502383.1
LSP1	ENST00000311604.8 link	c.-303G>A		upstream_gene_variant		1	NM_002339.3	ENSP00000308383.4

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39496

AN:

151822

Hom.:

5707

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

3181

6361

9542

12722

15903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.260

AC:

39530

AN:

151924

Hom.:

5707

Cov.:

AF XY:

0.259

AC XY:

19244

AN XY:

74240

show subpopulations

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:

AN:

290

European-Non Finnish (NFE)

AF:

0.319

AC:

21661

AN:

67916

Other (OTH)

AF:

0.267

AC:

562

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

1388

2776

4164

5552

6940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

(source)

DANN

Benign

0.90

PhyloP100

-0.47

PromoterAI

-0.33

Neutral

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over