14-92732735-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005606.7(LGMN):c.52G>A(p.Val18Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,613,640 control chromosomes in the GnomAD database, including 28,202 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005606.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGMN | NM_005606.7 | c.52G>A | p.Val18Ile | missense_variant | 2/14 | ENST00000334869.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGMN | ENST00000334869.9 | c.52G>A | p.Val18Ile | missense_variant | 2/14 | 1 | NM_005606.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.214 AC: 32525AN: 151976Hom.: 3694 Cov.: 32
GnomAD3 exomes AF: 0.198 AC: 49732AN: 251330Hom.: 5317 AF XY: 0.191 AC XY: 25966AN XY: 135834
GnomAD4 exome AF: 0.179 AC: 262231AN: 1461546Hom.: 24500 Cov.: 33 AF XY: 0.178 AC XY: 129743AN XY: 727106
GnomAD4 genome AF: 0.214 AC: 32550AN: 152094Hom.: 3702 Cov.: 32 AF XY: 0.216 AC XY: 16025AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at