13-75621829-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NR_120412.1(LMO7-AS1):n.166+14000C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,608,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
LMO7-AS1
NR_120412.1 intron, non_coding_transcript
NR_120412.1 intron, non_coding_transcript
Scores
2
1
14
Clinical Significance
Conservation
PhyloP100: 0.587
Genes affected
LMO7 (HGNC:6646): (LIM domain 7) This gene encodes a protein containing a calponin homology (CH) domain, a PDZ domain, and a LIM domain, and may be involved in protein-protein interactions. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene, however, the full-length nature of some variants is not known. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11013782).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMO7-AS1 | NR_120412.1 | n.166+14000C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMO7 | ENST00000341547.8 | c.136G>C | p.Gly46Arg | missense_variant | 1/30 | 1 | ENSP00000342112 | |||
LMO7-AS1 | ENST00000568302.5 | n.167-2923C>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
LMO7 | ENST00000357063.7 | c.91G>C | p.Gly31Arg | missense_variant | 1/32 | 5 | ENSP00000349571 | A2 | ||
LMO7-AS1 | ENST00000568735.1 | n.210+431C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249422Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134864
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GnomAD4 exome AF: 0.0000199 AC: 29AN: 1456532Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 20AN XY: 724500
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74280
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.136G>C (p.G46R) alteration is located in exon 1 (coding exon 1) of the LMO7 gene. This alteration results from a G to C substitution at nucleotide position 136, causing the glycine (G) at amino acid position 46 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;N
MutationTaster
Benign
N;N;N
PROVEAN
Benign
.;N
REVEL
Benign
Sift
Pathogenic
.;D
Sift4G
Pathogenic
D;D
Polyphen
0.69
.;P
Vest4
MVP
ClinPred
T
GERP RS
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