NM_001008212.2:c.293T>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001008212.2(OPTN):c.293T>A(p.Met98Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 1,614,026 control chromosomes in the GnomAD database, including 1,623 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001008212.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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OPTN | NM_001008212.2 | c.293T>A | p.Met98Lys | missense_variant | Exon 4 of 15 | ENST00000378747.8 | NP_001008213.1 | |
OPTN | NM_001008211.1 | c.293T>A | p.Met98Lys | missense_variant | Exon 5 of 16 | NP_001008212.1 | ||
OPTN | NM_001008213.1 | c.293T>A | p.Met98Lys | missense_variant | Exon 5 of 16 | NP_001008214.1 | ||
OPTN | NM_021980.4 | c.293T>A | p.Met98Lys | missense_variant | Exon 3 of 14 | NP_068815.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0591 AC: 8982AN: 152102Hom.: 373 Cov.: 32
GnomAD3 exomes AF: 0.0442 AC: 11112AN: 251306Hom.: 417 AF XY: 0.0430 AC XY: 5846AN XY: 135850
GnomAD4 exome AF: 0.0348 AC: 50846AN: 1461806Hom.: 1247 Cov.: 33 AF XY: 0.0351 AC XY: 25532AN XY: 727196
GnomAD4 genome AF: 0.0590 AC: 8982AN: 152220Hom.: 376 Cov.: 32 AF XY: 0.0593 AC XY: 4413AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:5
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not provided Benign:4
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This variant is associated with the following publications: (PMID: 16358725, 17361544, 31198474, 31182772, 17293779, 28430856, 26376340, 25681989, 15226658, 11834836, 19172505, 17122126, 23357852) -
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Primary open angle glaucoma Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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Glaucoma 1, open angle, E Pathogenic:1
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Amyotrophic lateral sclerosis type 12 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Primary open angle glaucoma;C1842026:Glaucoma 1, open angle, E;C3150692:Amyotrophic lateral sclerosis type 12 Benign:1
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Primary open angle glaucoma;C1847730:Glaucoma, normal tension, susceptibility to;C3150692:Amyotrophic lateral sclerosis type 12 Benign:1
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Glaucoma, normal tension, susceptibility to Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at