rs11342
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002298.5(LCP1):c.*1084C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000172 in 232,146 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
LCP1
NM_002298.5 3_prime_UTR
NM_002298.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.219
Publications
11 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LCP1 | NM_002298.5 | c.*1084C>T | 3_prime_UTR_variant | Exon 16 of 16 | ENST00000323076.7 | NP_002289.2 | ||
| LCP1 | XM_005266374.3 | c.*1084C>T | 3_prime_UTR_variant | Exon 16 of 16 | XP_005266431.1 | |||
| LCP1 | XM_047430303.1 | c.*1084C>T | 3_prime_UTR_variant | Exon 16 of 16 | XP_047286259.1 | |||
| LCP1 | XM_047430304.1 | c.*1084C>T | 3_prime_UTR_variant | Exon 14 of 14 | XP_047286260.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LCP1 | ENST00000323076.7 | c.*1084C>T | 3_prime_UTR_variant | Exon 16 of 16 | 1 | NM_002298.5 | ENSP00000315757.2 | |||
| LCP1 | ENST00000398576.6 | c.*1084C>T | 3_prime_UTR_variant | Exon 19 of 19 | 5 | ENSP00000381581.1 | ||||
| LCP1 | ENST00000674665.1 | c.*1084C>T | 3_prime_UTR_variant | Exon 5 of 5 | ENSP00000501964.1 | |||||
| CPB2-AS1 | ENST00000663159.1 | n.470-24987G>A | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 151952Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151952
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000125 AC: 1AN: 80194Hom.: 0 Cov.: 0 AF XY: 0.0000270 AC XY: 1AN XY: 37006 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
80194
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
37006
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
3838
American (AMR)
AF:
AC:
0
AN:
2448
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5074
East Asian (EAS)
AF:
AC:
0
AN:
11238
South Asian (SAS)
AF:
AC:
0
AN:
694
European-Finnish (FIN)
AF:
AC:
0
AN:
498
Middle Eastern (MID)
AF:
AC:
0
AN:
480
European-Non Finnish (NFE)
AF:
AC:
1
AN:
49264
Other (OTH)
AF:
AC:
0
AN:
6660
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000197 AC: 3AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74218 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151952
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74218
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41342
American (AMR)
AF:
AC:
1
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5174
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10564
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67974
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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