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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: 19-38499961-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38499961&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RYR1",
"hgnc_id": 10483,
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"inheritance_mode": "AD,AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_000540.3",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PP3_Strong,PP5",
"acmg_score": 7,
"allele_count_reference_population": 66,
"alphamissense_prediction": null,
"alphamissense_score": 0.9808,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.53,
"chr": "19",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 1, susceptibility to,Central core myopathy,Clubfoot,Congenital multicore myopathy with external ophthalmoplegia,Congenital myopathy with fiber type disproportion,EMG abnormality,King Denborough syndrome,Lower limb amyotrophy,Malignant hyperthermia,Neuromuscular disease,RYR1-related disorder,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:5 LP:3 US:1 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9548705220222473,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5038,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15400,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15117,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 106,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "NM_000540.3",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000359596.8",
"protein_coding": true,
"protein_id": "NP_000531.2",
"strand": true,
"transcript": "NM_000540.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5038,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15400,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15117,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 106,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000359596.8",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000540.3",
"protein_coding": true,
"protein_id": "ENSP00000352608.2",
"strand": true,
"transcript": "ENST00000359596.8",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5033,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15377,
"cdna_start": 7399,
"cds_end": null,
"cds_length": 15102,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000355481.8",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000347667.3",
"strand": true,
"transcript": "ENST00000355481.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 15347,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 103,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000594335.6",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "n.7268T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000470927.2",
"strand": true,
"transcript": "ENST00000594335.6",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5033,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15385,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15102,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "NM_001042723.2",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001036188.1",
"strand": true,
"transcript": "NM_001042723.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5009,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15169,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15030,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000689936.2",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508999.2",
"strand": true,
"transcript": "ENST00000689936.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 4993,
"aa_ref": "M",
"aa_start": 2383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15257,
"cdna_start": 7279,
"cds_end": null,
"cds_length": 14982,
"cds_start": 7148,
"consequences": [
"missense_variant"
],
"exon_count": 104,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "ENST00000713953.1",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7148T>A",
"hgvs_p": "p.Met2383Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519246.1",
"strand": true,
"transcript": "ENST00000713953.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 4927,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15067,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 14784,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000713952.1",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519245.1",
"strand": true,
"transcript": "ENST00000713952.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5032,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15382,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15099,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_006723317.3",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006723380.1",
"strand": true,
"transcript": "XM_006723317.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5027,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15367,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15084,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 104,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_006723319.3",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006723382.1",
"strand": true,
"transcript": "XM_006723319.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 5009,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15313,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 15030,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_011527205.3",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525507.1",
"strand": true,
"transcript": "XM_011527205.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 3068,
"aa_ref": "M",
"aa_start": 2423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9561,
"cdna_start": 7407,
"cds_end": null,
"cds_length": 9207,
"cds_start": 7268,
"consequences": [
"missense_variant"
],
"exon_count": 62,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_047439202.1",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "c.7268T>A",
"hgvs_p": "p.Met2423Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295158.1",
"strand": true,
"transcript": "XM_047439202.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 15308,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 104,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000593322.2",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "n.7268T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000471404.2",
"strand": true,
"transcript": "ENST00000593322.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 15200,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000599547.7",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "n.7268T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000471601.2",
"strand": true,
"transcript": "ENST00000599547.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 15322,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 105,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000688602.2",
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"hgvs_c": "n.7268T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510767.2",
"strand": true,
"transcript": "ENST00000688602.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs118192174",
"effect": "missense_variant",
"frequency_reference_population": 0.000040937848,
"gene_hgnc_id": 10483,
"gene_symbol": "RYR1",
"gnomad_exomes_ac": 63,
"gnomad_exomes_af": 0.0000431155,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000198665,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Congenital multicore myopathy with external ophthalmoplegia|not provided|Clubfoot;EMG abnormality;Lower limb amyotrophy|Congenital myopathy with fiber type disproportion|RYR1-related disorder|King Denborough syndrome;Congenital myopathy with fiber type disproportion;Malignant hyperthermia, susceptibility to, 1;Congenital multicore myopathy with external ophthalmoplegia;Central core myopathy|Malignant hyperthermia, susceptibility to, 1|Neuromuscular disease|Central core myopathy",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.001,
"pos": 38499961,
"ref": "T",
"revel_prediction": "Pathogenic",
"revel_score": 0.974,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000540.3"
}
]
}