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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: 9-5126410-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=5126410&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 5126410,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004972.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "NM_004972.4",
"protein_id": "NP_004963.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3722,
"cdna_end": null,
"cdna_length": 7023,
"mane_select": "ENST00000381652.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "ENST00000381652.4",
"protein_id": "ENSP00000371067.4",
"transcript_support_level": 1,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3722,
"cdna_end": null,
"cdna_length": 7023,
"mane_select": "NM_004972.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "NM_001322194.2",
"protein_id": "NP_001309123.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3850,
"cdna_end": null,
"cdna_length": 7151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "NM_001322195.2",
"protein_id": "NP_001309124.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3368,
"cdna_end": null,
"cdna_length": 6669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "NM_001322196.2",
"protein_id": "NP_001309125.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3639,
"cdna_end": null,
"cdna_length": 6940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.2808T>A",
"hgvs_p": "p.Asn936Lys",
"transcript": "NM_001322204.2",
"protein_id": "NP_001309133.1",
"transcript_support_level": null,
"aa_start": 936,
"aa_end": null,
"aa_length": 983,
"cds_start": 2808,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 3281,
"cdna_end": null,
"cdna_length": 6582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.2040T>A",
"hgvs_p": "p.Asn680Lys",
"transcript": "NM_001322198.2",
"protein_id": "NP_001309127.1",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 727,
"cds_start": 2040,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 3627,
"cdna_end": null,
"cdna_length": 6928,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "c.2040T>A",
"hgvs_p": "p.Asn680Lys",
"transcript": "NM_001322199.2",
"protein_id": "NP_001309128.1",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 727,
"cds_start": 2040,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 3569,
"cdna_end": null,
"cdna_length": 6870,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "n.446T>A",
"hgvs_p": null,
"transcript": "ENST00000487310.1",
"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": 773,
"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": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "n.3739T>A",
"hgvs_p": null,
"transcript": "NR_169763.1",
"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": 7040,
"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": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"hgvs_c": "n.3656T>A",
"hgvs_p": null,
"transcript": "NR_169764.1",
"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": 6957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "INSL6",
"gene_hgnc_id": 6089,
"hgvs_c": "c.*11-1899A>T",
"hgvs_p": null,
"transcript": "ENST00000649639.1",
"protein_id": "ENSP00000497955.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "INSL6",
"gene_hgnc_id": 6089,
"hgvs_c": "c.376+37769A>T",
"hgvs_p": null,
"transcript": "XM_011517702.4",
"protein_id": "XP_011516004.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 126,
"cds_start": -4,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JAK2",
"gene_hgnc_id": 6192,
"dbsnp": "rs1415418924",
"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": 0.33284974098205566,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.289,
"revel_prediction": "Benign",
"alphamissense_score": 0.1536,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.518,
"phylop100way_prediction": "Benign",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004972.4",
"gene_symbol": "JAK2",
"hgnc_id": 6192,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3255T>A",
"hgvs_p": "p.Asn1085Lys"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000649639.1",
"gene_symbol": "INSL6",
"hgnc_id": 6089,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*11-1899A>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}