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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: 5-87390806-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=87390806&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 87390806,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000274376.11",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.3067T>A",
"hgvs_p": "p.Leu1023Met",
"transcript": "NM_002890.3",
"protein_id": "NP_002881.1",
"transcript_support_level": null,
"aa_start": 1023,
"aa_end": null,
"aa_length": 1047,
"cds_start": 3067,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 3636,
"cdna_end": null,
"cdna_length": 4746,
"mane_select": "ENST00000274376.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.3067T>A",
"hgvs_p": "p.Leu1023Met",
"transcript": "ENST00000274376.11",
"protein_id": "ENSP00000274376.6",
"transcript_support_level": 1,
"aa_start": 1023,
"aa_end": null,
"aa_length": 1047,
"cds_start": 3067,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 3636,
"cdna_end": null,
"cdna_length": 4746,
"mane_select": "NM_002890.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.2536T>A",
"hgvs_p": "p.Leu846Met",
"transcript": "ENST00000456692.6",
"protein_id": "ENSP00000411221.2",
"transcript_support_level": 1,
"aa_start": 846,
"aa_end": null,
"aa_length": 870,
"cds_start": 2536,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2651,
"cdna_end": null,
"cdna_length": 3776,
"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": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "n.*1682T>A",
"hgvs_p": null,
"transcript": "ENST00000515800.6",
"protein_id": "ENSP00000423395.2",
"transcript_support_level": 1,
"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": 4979,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "n.*1682T>A",
"hgvs_p": null,
"transcript": "ENST00000515800.6",
"protein_id": "ENSP00000423395.2",
"transcript_support_level": 1,
"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": 4979,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.2569T>A",
"hgvs_p": "p.Leu857Met",
"transcript": "ENST00000506290.1",
"protein_id": "ENSP00000420905.1",
"transcript_support_level": 2,
"aa_start": 857,
"aa_end": null,
"aa_length": 881,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 2686,
"cdna_end": null,
"cdna_length": 3009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.2566T>A",
"hgvs_p": "p.Leu856Met",
"transcript": "ENST00000512763.5",
"protein_id": "ENSP00000422008.1",
"transcript_support_level": 2,
"aa_start": 856,
"aa_end": null,
"aa_length": 880,
"cds_start": 2566,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 2767,
"cdna_end": null,
"cdna_length": 3060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"hgvs_c": "c.2536T>A",
"hgvs_p": "p.Leu846Met",
"transcript": "NM_022650.3",
"protein_id": "NP_072179.1",
"transcript_support_level": null,
"aa_start": 846,
"aa_end": null,
"aa_length": 870,
"cds_start": 2536,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2647,
"cdna_end": null,
"cdna_length": 3757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.3004A>T",
"hgvs_p": null,
"transcript": "NR_157071.2",
"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": 4214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "c.*2054A>T",
"hgvs_p": null,
"transcript": "NM_001363539.2",
"protein_id": "NP_001350468.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "c.*2054A>T",
"hgvs_p": null,
"transcript": "NM_001364076.2",
"protein_id": "NP_001351005.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 272,
"cds_start": -4,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4621,
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "c.933+4238A>T",
"hgvs_p": null,
"transcript": "NM_001364075.2",
"protein_id": "NP_001351004.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.*90+1964A>T",
"hgvs_p": null,
"transcript": "ENST00000645953.1",
"protein_id": "ENSP00000494460.1",
"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": 1664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.*90+1964A>T",
"hgvs_p": null,
"transcript": "ENST00000646883.1",
"protein_id": "ENSP00000493789.1",
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.1447+1964A>T",
"hgvs_p": null,
"transcript": "NR_157068.2",
"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": 2772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.1040+1964A>T",
"hgvs_p": null,
"transcript": "NR_157069.2",
"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": 2365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "CCNH",
"gene_hgnc_id": 1594,
"hgvs_c": "n.1204+1964A>T",
"hgvs_p": null,
"transcript": "NR_157070.2",
"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": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RASA1",
"gene_hgnc_id": 9871,
"dbsnp": "rs3747704",
"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": 0.28520137071609497,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.228,
"revel_prediction": "Benign",
"alphamissense_score": 0.5597,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.432,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": "ENST00000274376.11",
"gene_symbol": "RASA1",
"hgnc_id": 9871,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3067T>A",
"hgvs_p": "p.Leu1023Met"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NR_157071.2",
"gene_symbol": "CCNH",
"hgnc_id": 1594,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.3004A>T",
"hgvs_p": null
}
],
"clinvar_disease": "Capillary malformation-arteriovenous malformation syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Capillary malformation-arteriovenous malformation syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}