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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: 19-38496466-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38496466&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 38496466,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_000540.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 106,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "NM_000540.3",
"protein_id": "NP_000531.2",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5038,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359596.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000540.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 106,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "ENST00000359596.8",
"protein_id": "ENSP00000352608.2",
"transcript_support_level": 5,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5038,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000540.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359596.8"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "ENST00000355481.8",
"protein_id": "ENSP00000347667.3",
"transcript_support_level": 1,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5033,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355481.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 103,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "n.6721C>T",
"hgvs_p": null,
"transcript": "ENST00000594335.6",
"protein_id": "ENSP00000470927.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000594335.6"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "NM_001042723.2",
"protein_id": "NP_001036188.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5033,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042723.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "ENST00000689936.2",
"protein_id": "ENSP00000508999.2",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5009,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000689936.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 104,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6601C>T",
"hgvs_p": "p.Arg2201*",
"transcript": "ENST00000713953.1",
"protein_id": "ENSP00000519246.1",
"transcript_support_level": null,
"aa_start": 2201,
"aa_end": null,
"aa_length": 4993,
"cds_start": 6601,
"cds_end": null,
"cds_length": 14982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713953.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "ENST00000713952.1",
"protein_id": "ENSP00000519245.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 4927,
"cds_start": 6721,
"cds_end": null,
"cds_length": 14784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713952.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "XM_006723317.3",
"protein_id": "XP_006723380.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5032,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723317.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 104,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "XM_006723319.3",
"protein_id": "XP_006723382.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5027,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15084,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723319.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "XM_011527205.3",
"protein_id": "XP_011525507.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 5009,
"cds_start": 6721,
"cds_end": null,
"cds_length": 15030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527205.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*",
"transcript": "XM_047439202.1",
"protein_id": "XP_047295158.1",
"transcript_support_level": null,
"aa_start": 2241,
"aa_end": null,
"aa_length": 3068,
"cds_start": 6721,
"cds_end": null,
"cds_length": 9207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439202.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 104,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "n.6721C>T",
"hgvs_p": null,
"transcript": "ENST00000593322.2",
"protein_id": "ENSP00000471404.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000593322.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "n.6721C>T",
"hgvs_p": null,
"transcript": "ENST00000599547.7",
"protein_id": "ENSP00000471601.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000599547.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 105,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"hgvs_c": "n.6721C>T",
"hgvs_p": null,
"transcript": "ENST00000688602.2",
"protein_id": "ENSP00000510767.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000688602.2"
}
],
"gene_symbol": "RYR1",
"gene_hgnc_id": 10483,
"dbsnp": "rs200563280",
"frequency_reference_population": 0.00016111841,
"hom_count_reference_population": 0,
"allele_count_reference_population": 260,
"gnomad_exomes_af": 0.000160796,
"gnomad_genomes_af": 0.000164212,
"gnomad_exomes_ac": 235,
"gnomad_genomes_ac": 25,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.809,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000540.3",
"gene_symbol": "RYR1",
"hgnc_id": 10483,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.6721C>T",
"hgvs_p": "p.Arg2241*"
}
],
"clinvar_disease": " 1, susceptibility to,Central core myopathy,Congenital multicore myopathy with external ophthalmoplegia,Congenital myopathy with fiber type disproportion,Hydrops fetalis,King Denborough syndrome,Malignant hyperthermia,Multi-minicore disease and atypical periodic paralysis,Neuromuscular disease,RYR1-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:19 LP:1 US:1 LB:1",
"phenotype_combined": "RYR1-related disorder|not provided|Malignant hyperthermia, susceptibility to, 1|Central core myopathy;Neuromuscular disease|Multi-minicore disease and atypical periodic paralysis|Congenital multicore myopathy with external ophthalmoplegia|Hydrops fetalis|Central core myopathy;Congenital multicore myopathy with external ophthalmoplegia;King Denborough syndrome;Malignant hyperthermia, susceptibility to, 1|Central core myopathy|Central core myopathy;Congenital multicore myopathy with external ophthalmoplegia;Congenital myopathy with fiber type disproportion;King Denborough syndrome;Malignant hyperthermia, susceptibility to, 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}