rs2089910
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002339.3(LSP1):c.30C>T(p.Ala10Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,610,092 control chromosomes in the GnomAD database, including 48,041 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 ( 5433 hom., cov: 33)
Exomes 𝑓: 0.24 ( 42608 hom. )
Consequence
LSP1
NM_002339.3 synonymous
NM_002339.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.96
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=-3.96 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LSP1 | NM_002339.3 | c.30C>T | p.Ala10Ala | synonymous_variant | 1/11 | ENST00000311604.8 | NP_002330.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LSP1 | ENST00000311604.8 | c.30C>T | p.Ala10Ala | synonymous_variant | 1/11 | 1 | NM_002339.3 | ENSP00000308383.4 | ||
LSP1 | ENST00000676039.1 | c.30C>T | p.Ala10Ala | synonymous_variant | 2/2 | ENSP00000502383.1 |
Frequencies
GnomAD3 genomes AF: 0.261 AC: 39723AN: 151968Hom.: 5439 Cov.: 33
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GnomAD3 exomes AF: 0.258 AC: 61511AN: 238024Hom.: 8431 AF XY: 0.253 AC XY: 32742AN XY: 129260
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GnomAD4 exome AF: 0.237 AC: 346169AN: 1458006Hom.: 42608 Cov.: 34 AF XY: 0.236 AC XY: 171463AN XY: 725058
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GnomAD4 genome AF: 0.261 AC: 39743AN: 152086Hom.: 5433 Cov.: 33 AF XY: 0.265 AC XY: 19706AN XY: 74354
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at