rs10937595
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_130837.3(OPA1):c.2872+25T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 1,514,964 control chromosomes in the GnomAD database, including 141,876 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.42 ( 13962 hom., cov: 32)
Exomes 𝑓: 0.43 ( 127914 hom. )
Consequence
OPA1
NM_130837.3 intron
NM_130837.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.247
Genes affected
OPA1 (HGNC:8140): (OPA1 mitochondrial dynamin like GTPase) The protein encoded by this gene is a nuclear-encoded mitochondrial protein with similarity to dynamin-related GTPases. The encoded protein localizes to the inner mitochondrial membrane and helps regulate mitochondrial stability and energy output. This protein also sequesters cytochrome c. Mutations in this gene have been associated with optic atrophy type 1, which is a dominantly inherited optic neuropathy resulting in progressive loss of visual acuity, leading in many cases to legal blindness. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 3-193666414-T-A is Benign according to our data. Variant chr3-193666414-T-A is described in ClinVar as [Benign]. Clinvar id is 1291406.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-193666414-T-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPA1 | NM_130837.3 | c.2872+25T>A | intron_variant | ENST00000361510.8 | |||
LOC102724808 | XR_924835.3 | n.420+2506A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPA1 | ENST00000361510.8 | c.2872+25T>A | intron_variant | 5 | NM_130837.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.424 AC: 64400AN: 151968Hom.: 13953 Cov.: 32
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GnomAD3 exomes AF: 0.422 AC: 105860AN: 250798Hom.: 22889 AF XY: 0.419 AC XY: 56776AN XY: 135542
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GnomAD4 exome AF: 0.430 AC: 585894AN: 1362878Hom.: 127914 Cov.: 21 AF XY: 0.428 AC XY: 292298AN XY: 683642
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GnomAD4 genome ? AF: 0.424 AC: 64454AN: 152086Hom.: 13962 Cov.: 32 AF XY: 0.426 AC XY: 31673AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at