rs370955995
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4BP6BS1BS2
The NM_005097.4(LGI1):c.1669G>A(p.Ala557Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000282 in 1,597,842 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A557A) has been classified as Likely benign.
Frequency
Consequence
NM_005097.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGI1 | NM_005097.4 | c.1669G>A | p.Ala557Thr | missense_variant | 8/8 | ENST00000371418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGI1 | ENST00000371418.9 | c.1669G>A | p.Ala557Thr | missense_variant | 8/8 | 1 | NM_005097.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000380 AC: 9AN: 236852Hom.: 0 AF XY: 0.0000386 AC XY: 5AN XY: 129556
GnomAD4 exome AF: 0.0000242 AC: 35AN: 1445572Hom.: 0 Cov.: 30 AF XY: 0.0000236 AC XY: 17AN XY: 719764
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74448
ClinVar
Submissions by phenotype
Autosomal dominant epilepsy with auditory features Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 08, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 557 of the LGI1 protein (p.Ala557Thr). This variant is present in population databases (rs370955995, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with LGI1-related conditions. ClinVar contains an entry for this variant (Variation ID: 206032). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 20, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at