13-75713189-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001306080.2(LMO7):c.77C>A(p.Thr26Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000223 in 1,611,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001306080.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMO7 | NM_001306080.2 | c.77C>A | p.Thr26Lys | missense_variant | Exon 2 of 31 | ENST00000377534.8 | NP_001293009.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250598Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135488
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459656Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 726230
GnomAD4 genome AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.233C>A (p.T78K) alteration is located in exon 3 (coding exon 3) of the LMO7 gene. This alteration results from a C to A substitution at nucleotide position 233, causing the threonine (T) at amino acid position 78 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at