rs2146880
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002298.5(LCP1):c.1627-1525G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,988 control chromosomes in the GnomAD database, including 14,326 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 0.43 ( 14326 hom., cov: 31)
Consequence
LCP1
NM_002298.5 intron
NM_002298.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.758
Genes affected
LCP1 (HGNC:6528): (lymphocyte cytosolic protein 1) Plastins are a family of actin-binding proteins that are conserved throughout eukaryote evolution and expressed in most tissues of higher eukaryotes. In humans, two ubiquitous plastin isoforms (L and T) have been identified. Plastin 1 (otherwise known as Fimbrin) is a third distinct plastin isoform which is specifically expressed at high levels in the small intestine. The L isoform is expressed only in hemopoietic cell lineages, while the T isoform has been found in all other normal cells of solid tissues that have replicative potential (fibroblasts, endothelial cells, epithelial cells, melanocytes, etc.). However, L-plastin has been found in many types of malignant human cells of non-hemopoietic origin suggesting that its expression is induced accompanying tumorigenesis in solid tissues. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCP1 | NM_002298.5 | c.1627-1525G>T | intron_variant | ENST00000323076.7 | |||
LCP1 | XM_005266374.3 | c.1627-1525G>T | intron_variant | ||||
LCP1 | XM_047430303.1 | c.1627-1525G>T | intron_variant | ||||
LCP1 | XM_047430304.1 | c.1192-1525G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCP1 | ENST00000323076.7 | c.1627-1525G>T | intron_variant | 1 | NM_002298.5 | P1 | |||
CPB2-AS1 | ENST00000663159.1 | n.470-19031C>A | intron_variant, non_coding_transcript_variant | ||||||
LCP1 | ENST00000398576.6 | c.1627-1525G>T | intron_variant | 5 | P1 | ||||
LCP1 | ENST00000674665.1 | c.334-1525G>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.429 AC: 65210AN: 151870Hom.: 14312 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.429 AC: 65268AN: 151988Hom.: 14326 Cov.: 31 AF XY: 0.434 AC XY: 32220AN XY: 74294
GnomAD4 genome
?
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151988
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31
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32220
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74294
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1513
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at