chr12-50195891-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_016357.5(LIMA1):c.973-4G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.14 ( 0 hom., cov: 0)
Exomes 𝑓: 0.038 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
LIMA1
NM_016357.5 splice_region, splice_polypyrimidine_tract, intron
NM_016357.5 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00008505
2
Clinical Significance
Conservation
PhyloP100: 0.101
Genes affected
LIMA1 (HGNC:24636): (LIM domain and actin binding 1) This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 12-50195891-C-A is Benign according to our data. Variant chr12-50195891-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3042369.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAdExome at 4251 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIMA1 | NM_016357.5 | c.973-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000341247.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIMA1 | ENST00000341247.9 | c.973-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016357.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 5625AN: 39528Hom.: 0 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.197 AC: 4251AN: 21594Hom.: 0 AF XY: 0.210 AC XY: 2422AN XY: 11558
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0381 AC: 39612AN: 1039840Hom.: 2 Cov.: 21 AF XY: 0.0373 AC XY: 19036AN XY: 510760
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.142 AC: 5623AN: 39530Hom.: 0 Cov.: 0 AF XY: 0.129 AC XY: 2439AN XY: 18970
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
LIMA1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 03, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at