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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: 19-10819992-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=10819992&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 10819992,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001005361.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "NM_001005361.3",
"protein_id": "NP_001005361.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 870,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "ENST00000389253.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "ENST00000389253.9",
"protein_id": "ENSP00000373905.4",
"transcript_support_level": 5,
"aa_start": 562,
"aa_end": null,
"aa_length": 870,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "NM_001005361.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "ENST00000355667.11",
"protein_id": "ENSP00000347890.6",
"transcript_support_level": 1,
"aa_start": 562,
"aa_end": null,
"aa_length": 870,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "ENST00000585892.5",
"protein_id": "ENSP00000468734.1",
"transcript_support_level": 1,
"aa_start": 562,
"aa_end": null,
"aa_length": 869,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 2774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1672A>G",
"hgvs_p": "p.Lys558Glu",
"transcript": "ENST00000359692.10",
"protein_id": "ENSP00000352721.6",
"transcript_support_level": 1,
"aa_start": 558,
"aa_end": null,
"aa_length": 866,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1822,
"cdna_end": null,
"cdna_length": 3588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "NM_001005360.3",
"protein_id": "NP_001005360.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 870,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu",
"transcript": "NM_001190716.2",
"protein_id": "NP_001177645.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 869,
"cds_start": 1684,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1672A>G",
"hgvs_p": "p.Lys558Glu",
"transcript": "NM_001005362.3",
"protein_id": "NP_001005362.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 866,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 3621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1672A>G",
"hgvs_p": "p.Lys558Glu",
"transcript": "NM_004945.4",
"protein_id": "NP_004936.2",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 866,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 3621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.1672A>G",
"hgvs_p": "p.Lys558Glu",
"transcript": "ENST00000408974.8",
"protein_id": "ENSP00000386192.3",
"transcript_support_level": 2,
"aa_start": 558,
"aa_end": null,
"aa_length": 866,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1707,
"cdna_end": null,
"cdna_length": 3013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.3183A>G",
"hgvs_p": null,
"transcript": "ENST00000590787.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.3872A>G",
"hgvs_p": null,
"transcript": "ENST00000590806.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.1115A>G",
"hgvs_p": null,
"transcript": "ENST00000681972.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"dbsnp": "rs121909088",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9237696528434753,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.792,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9979,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.234,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001005361.3",
"gene_symbol": "DNM2",
"hgnc_id": 2974,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1684A>G",
"hgvs_p": "p.Lys562Glu"
}
],
"clinvar_disease": " dominant intermediate B, with neutropenia,Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease dominant intermediate B",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Charcot-Marie-Tooth disease, dominant intermediate B, with neutropenia|Charcot-Marie-Tooth disease|Charcot-Marie-Tooth disease dominant intermediate B",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}