8-22148657-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_139278.4(LGI3):c.1150G>A(p.Gly384Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,614,014 control chromosomes in the GnomAD database, including 146 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_139278.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGI3 | ENST00000306317.7 | c.1150G>A | p.Gly384Ser | missense_variant | Exon 8 of 8 | 1 | NM_139278.4 | ENSP00000302297.2 | ||
LGI3 | ENST00000424267.6 | c.1078G>A | p.Gly360Ser | missense_variant | Exon 7 of 7 | 1 | ENSP00000399121.2 | |||
LGI3 | ENST00000520124.5 | n.2593G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00460 AC: 700AN: 152160Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.0111 AC: 2796AN: 251116Hom.: 108 AF XY: 0.00855 AC XY: 1161AN XY: 135760
GnomAD4 exome AF: 0.00252 AC: 3690AN: 1461736Hom.: 129 Cov.: 32 AF XY: 0.00220 AC XY: 1597AN XY: 727168
GnomAD4 genome AF: 0.00463 AC: 705AN: 152278Hom.: 17 Cov.: 32 AF XY: 0.00474 AC XY: 353AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at