Genetic Variant LSP1:c.591+38T>C (chr11-1884062-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002339.3(LSP1):c.591+38T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 1,574,862 control chromosomes in the GnomAD database, including 141,011 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 0.38 ( 12094 hom., cov: 31)

Exomes 𝑓: 0.42 ( 128917 hom. )

Consequence

LSP1
NM_002339.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.192

Publications

36 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:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LSP1	NM_002339.3	MANE Select	c.591+38T>C	intron	N/A	NP_002330.1
LSP1	NM_001242932.2		c.975+38T>C	intron	N/A	NP_001229861.1
LSP1	NM_001013253.2		c.405+38T>C	intron	N/A	NP_001013271.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LSP1	ENST00000311604.8	TSL:1 MANE Select	c.591+38T>C	intron	N/A	ENSP00000308383.4
LSP1	ENST00000381775.5	TSL:2	c.975+38T>C	intron	N/A	ENSP00000371194.1
LSP1	ENST00000405957.6	TSL:5	c.405+38T>C	intron	N/A	ENSP00000383932.2

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57192

AN:

151472

Hom.:

12088

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.383

GnomAD2 exomes

AF:

0.429

AC:

99337

AN:

231588

AF XY:

0.419

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.600

Gnomad ASJ exome

AF:

0.384

Gnomad EAS exome

AF:

0.596

Gnomad FIN exome

AF:

0.469

Gnomad NFE exome

AF:

0.425

Gnomad OTH exome

AF:

0.410

GnomAD4 exome

AF:

0.419

AC:

596287

AN:

1423284

Hom.:

128917

Cov.:

AF XY:

0.414

AC XY:

293113

AN XY:

707510

show subpopulations

African (AFR)

AF:

0.174

AC:

5586

AN:

32064

American (AMR)

AF:

0.592

AC:

23951

AN:

40486

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

9859

AN:

24792

East Asian (EAS)

AF:

0.584

AC:

23025

AN:

39438

South Asian (SAS)

AF:

0.281

AC:

23212

AN:

82614

European-Finnish (FIN)

AF:

0.474

AC:

24547

AN:

51804

Middle Eastern (MID)

AF:

0.352

AC:

1968

AN:

5598

European-Non Finnish (NFE)

AF:

0.423

AC:

460296

AN:

1087664

Other (OTH)

AF:

0.405

AC:

23843

AN:

58824

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

17599

35198

52796

70395

87994

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13976

27952

41928

55904

69880

<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:

0.377

AC:

57215

AN:

151578

Hom.:

12094

Cov.:

AF XY:

0.382

AC XY:

28255

AN XY:

74030

show subpopulations

African (AFR)

AF:

0.186

AC:

7668

AN:

41284

American (AMR)

AF:

0.518

AC:

7908

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

1382

AN:

3466

East Asian (EAS)

AF:

0.589

AC:

3036

AN:

5154

South Asian (SAS)

AF:

0.307

AC:

1473

AN:

4792

European-Finnish (FIN)

AF:

0.472

AC:

4949

AN:

10484

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.432

AC:

29268

AN:

67822

Other (OTH)

AF:

0.380

AC:

799

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1697

3394

5092

6789

8486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

538

1076

1614

2152

2690

<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:

0.414

Hom.:

24990

Bravo

AF:

0.376

Asia WGS

AF:

0.459

AC:

1594

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.9

(source)

DANN

Benign

0.73

PhyloP100

0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over