Variant chr11-1881538-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002339.3(LSP1):c.298G>A(p.Ala100Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,545,222 control chromosomes in the GnomAD database, including 112,979 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.37 ( 10853 hom., cov: 34)

Exomes 𝑓: 0.38 ( 102126 hom. )

Consequence

LSP1
NM_002339.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

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:

LSP1 (HGNC:):

LSP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.4315276E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSP1	NM_002339.3 linkuse as main transcript	c.298G>A	p.Ala100Thr	missense_variant	3/11	ENST00000311604.8	NP_002330.1	P33241-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSP1	ENST00000311604.8 linkuse as main transcript	c.298G>A	p.Ala100Thr	missense_variant	3/11	1	NM_002339.3	ENSP00000308383.4		P33241-1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

55663

AN:

150852

Hom.:

10847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.506

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.382

GnomAD3 exomes

AF:

0.410

AC:

62454

AN:

152148

Hom.:

13901

AF XY:

0.398

AC XY:

32032

AN XY:

80476

show subpopulations

Gnomad AFR exome

AF:

0.265

Gnomad AMR exome

AF:

0.589

Gnomad ASJ exome

AF:

0.363

Gnomad EAS exome

AF:

0.581

Gnomad SAS exome

AF:

0.275

Gnomad FIN exome

AF:

0.419

Gnomad NFE exome

AF:

0.382

Gnomad OTH exome

AF:

0.399

GnomAD4 exome

AF:

0.377

AC:

525881

AN:

1394252

Hom.:

102126

Cov.:

AF XY:

0.374

AC XY:

257321

AN XY:

687746

show subpopulations

Gnomad4 AFR exome

AF:

0.262

Gnomad4 AMR exome

AF:

0.579

Gnomad4 ASJ exome

AF:

0.365

Gnomad4 EAS exome

AF:

0.563

Gnomad4 SAS exome

AF:

0.279

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.374

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.369

AC:

55699

AN:

150970

Hom.:

10853

Cov.:

AF XY:

0.372

AC XY:

27418

AN XY:

73744

show subpopulations

Gnomad4 AFR

AF:

0.271

Gnomad4 AMR

AF:

0.506

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.576

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.381

Alfa

AF:

0.372

Hom.:

5188

Bravo

AF:

0.377

TwinsUK

AF:

0.358

AC:

1328

ALSPAC

AF:

0.363

AC:

1400

ESP6500AA

AF:

0.267

AC:

1155

ESP6500EA

AF:

0.362

AC:

3046

ExAC

AF:

0.297

AC:

30181

Asia WGS

AF:

0.446

AC:

1542

AN:

3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.0050

DANN

Benign

0.26

DEOGEN2

Benign

0.044

T;.;T;.;.;T;.;.;T;.;.;T;T

Eigen

Benign

-2.4

Eigen_PC

Benign

-2.4

FATHMM_MKL

Benign

0.0032

LIST_S2

Benign

0.48

T;T;T;T;.;T;T;T;T;.;T;.;T

MetaRNN

Benign

0.000014

T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.29

N;.;.;.;.;.;.;.;.;.;.;.;.

PrimateAI

Benign

0.36

PROVEAN

Benign

0.97

N;N;N;N;N;N;N;N;N;N;.;N;N

REVEL

Benign

0.054

Sift

Benign

1.0

T;T;T;T;T;T;T;T;T;T;.;T;T

Sift4G

Benign

0.71

T;T;T;T;T;T;T;.;T;T;T;T;T

Polyphen

0.010

B;.;.;.;.;.;.;.;.;.;.;.;.

Vest4

0.0090

MPC

0.10

ClinPred

0.0018

GERP RS

-6.0

Varity_R

0.036

gMVP

0.021

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over