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GeneBe

rs3817198

Variant summary

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

The NM_002339.3(LSP1):c.*13+200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,994 control chromosomes in the GnomAD database, including 5,474 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 ( 5474 hom., cov: 32)

Consequence

LSP1
NM_002339.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107
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]

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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 (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LSP1NM_002339.3 linkuse as main transcriptc.*13+200T>C intron_variant ENST00000311604.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LSP1ENST00000311604.8 linkuse as main transcriptc.*13+200T>C intron_variant 1 NM_002339.3 P2P33241-1

Frequencies

GnomAD3 genomes
AF:
0.256
AC:
38942
AN:
151876
Hom.:
5475
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.260
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.112
Gnomad SAS
AF:
0.371
Gnomad FIN
AF:
0.235
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.256
AC:
38951
AN:
151994
Hom.:
5474
Cov.:
32
AF XY:
0.254
AC XY:
18868
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.162
Gnomad4 AMR
AF:
0.229
Gnomad4 ASJ
AF:
0.420
Gnomad4 EAS
AF:
0.112
Gnomad4 SAS
AF:
0.371
Gnomad4 FIN
AF:
0.235
Gnomad4 NFE
AF:
0.317
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.306
Hom.:
14120
Bravo
AF:
0.246
Asia WGS
AF:
0.215
AC:
750
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
0.96
Dann
Benign
0.82

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.

Other links and lift over

dbSNP: rs3817198; hg19: chr11-1909006; API