chr10-93792896-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005097.4(LGI1):āc.657T>Cā(p.Phe219=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.995 in 1,614,040 control chromosomes in the GnomAD database, including 799,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.98 ( 72926 hom., cov: 30)
Exomes š: 1.0 ( 726800 hom. )
Consequence
LGI1
NM_005097.4 synonymous
NM_005097.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.31
Genes affected
LGI1 (HGNC:6572): (leucine rich glioma inactivated 1) This gene encodes a member of the secreted leucine-rich repeat (LRR) superfamily and shares homology with members of the SLIT protein family. The encoded protein may regulate the activity of voltage-gated potassium channels and may be involved in neuronal growth regulation and cell survival. This gene is rearranged as a result of translocations in glioblastoma cell lines, and it is frequently down-regulated or rearranged in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 10-93792896-T-C is Benign according to our data. Variant chr10-93792896-T-C is described in ClinVar as [Benign]. Clinvar id is 1164242.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-93792896-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=2.31 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGI1 | NM_005097.4 | c.657T>C | p.Phe219= | synonymous_variant | 6/8 | ENST00000371418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGI1 | ENST00000371418.9 | c.657T>C | p.Phe219= | synonymous_variant | 6/8 | 1 | NM_005097.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.978 AC: 148821AN: 152104Hom.: 72880 Cov.: 30
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GnomAD3 exomes AF: 0.994 AC: 249854AN: 251436Hom.: 124178 AF XY: 0.995 AC XY: 135197AN XY: 135888
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GnomAD4 exome AF: 0.997 AC: 1457602AN: 1461818Hom.: 726800 Cov.: 49 AF XY: 0.997 AC XY: 725364AN XY: 727222
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GnomAD4 genome AF: 0.978 AC: 148923AN: 152222Hom.: 72926 Cov.: 30 AF XY: 0.979 AC XY: 72887AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal dominant epilepsy with auditory features Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Epilepsy, familial temporal lobe, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at