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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 22-38115657-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=38115657&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLA2G6",
"hgnc_id": 9039,
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_003560.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 12,
"allele_count_reference_population": 33,
"alphamissense_prediction": null,
"alphamissense_score": 0.9295,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"chr": "22",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Autosomal recessive Parkinson disease 14,Infantile neuroaxonal dystrophy,Neurodegeneration with brain iron accumulation 2B,PLA2G6-associated neurodegeneration,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8906305432319641,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3299,
"cdna_start": 2116,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_003560.4",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000332509.8",
"protein_coding": true,
"protein_id": "NP_003551.2",
"strand": false,
"transcript": "NM_003560.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3299,
"cdna_start": 2116,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000332509.8",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003560.4",
"protein_coding": true,
"protein_id": "ENSP00000333142.3",
"strand": false,
"transcript": "ENST00000332509.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 752,
"aa_ref": "R",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3011,
"cdna_start": 1833,
"cds_end": null,
"cds_length": 2259,
"cds_start": 1742,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000402064.5",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386100.1",
"strand": false,
"transcript": "ENST00000402064.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 820,
"aa_ref": "R",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2830,
"cdna_start": 1831,
"cds_end": null,
"cds_length": 2463,
"cds_start": 1742,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000668949.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499711.1",
"strand": false,
"transcript": "ENST00000668949.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3295,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001349864.2",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001336793.1",
"strand": false,
"transcript": "NM_001349864.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3195,
"cdna_start": 2271,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000660610.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499555.1",
"strand": false,
"transcript": "ENST00000660610.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3171,
"cdna_start": 1988,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000663895.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499712.1",
"strand": false,
"transcript": "ENST00000663895.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2813,
"cdna_start": 1966,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000667521.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499665.1",
"strand": false,
"transcript": "ENST00000667521.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3212,
"cdna_start": 2034,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000885143.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555202.1",
"strand": false,
"transcript": "ENST00000885143.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 806,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3285,
"cdna_start": 2102,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000885146.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1904G>A",
"hgvs_p": "p.Arg635Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555205.1",
"strand": false,
"transcript": "ENST00000885146.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 760,
"aa_ref": "R",
"aa_start": 589,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2959,
"cdna_start": 1863,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1766,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000664587.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1766G>A",
"hgvs_p": "p.Arg589Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499394.1",
"strand": false,
"transcript": "ENST00000664587.1",
"transcript_support_level": null
},
{
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"aa_length": 752,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3137,
"cdna_start": 1954,
"cds_end": null,
"cds_length": 2259,
"cds_start": 1742,
"consequences": [
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],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001004426.3",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001004426.1",
"strand": false,
"transcript": "NM_001004426.3",
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},
{
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"cds_end": null,
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"consequences": [
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],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001199562.3",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186491.1",
"strand": false,
"transcript": "NM_001199562.3",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3133,
"cdna_start": 1950,
"cds_end": null,
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"cds_start": 1742,
"consequences": [
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],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001349865.2",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001336794.1",
"strand": false,
"transcript": "NM_001349865.2",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3013,
"cdna_start": 1830,
"cds_end": null,
"cds_length": 2259,
"cds_start": 1742,
"consequences": [
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],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001349866.2",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001336795.1",
"strand": false,
"transcript": "NM_001349866.2",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": 1878,
"cds_end": null,
"cds_length": 2259,
"cds_start": 1742,
"consequences": [
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],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000335539.7",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000335149.3",
"strand": false,
"transcript": "ENST00000335539.7",
"transcript_support_level": 5
},
{
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"consequences": [
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],
"exon_count": 16,
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"feature": "ENST00000885144.1",
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"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
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},
{
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"cds_end": null,
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],
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"feature": "ENST00000885145.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
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"mane_plus": null,
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"protein_coding": true,
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"strand": false,
"transcript": "ENST00000885145.1",
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},
{
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"consequences": [
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],
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"exon_rank": 13,
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"feature": "ENST00000955628.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1742G>A",
"hgvs_p": "p.Arg581Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625687.1",
"strand": false,
"transcript": "ENST00000955628.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_ref": "R",
"aa_start": 571,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2965,
"cdna_start": 1787,
"cds_end": null,
"cds_length": 2229,
"cds_start": 1712,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000955632.1",
"gene_hgnc_id": 9039,
"gene_symbol": "PLA2G6",
"hgvs_c": "c.1712G>A",
"hgvs_p": "p.Arg571Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625691.1",
"strand": false,
"transcript": "ENST00000955632.1",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2928,
"cdna_start": 1750,
"cds_end": null,
"cds_length": 2205,
"cds_start": 1688,
"consequences": [
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},
{
"aa_alt": null,
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"biotype": "nonsense_mediated_decay",
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"3_prime_UTR_variant"
],
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"feature": "ENST00000673413.1",
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"protein_id": "ENSP00000500600.1",
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}
],
"custom_annotations": null,
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"dbscsnv_ada_score": null,
"dbsnp": "rs387906863",
"effect": "missense_variant",
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"gnomad_exomes_ac": 33,
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"gnomad_mito_homoplasmic": null,
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"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Autosomal recessive Parkinson disease 14|PLA2G6-associated neurodegeneration|not provided|Infantile neuroaxonal dystrophy;Neurodegeneration with brain iron accumulation 2B;Autosomal recessive Parkinson disease 14|Infantile neuroaxonal dystrophy",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.389,
"pos": 38115657,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.864,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
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"transcript": "NM_003560.4"
}
]
}