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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: 2-38986117-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=38986117&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 38986117,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005633.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3709C>T",
"hgvs_p": "p.Pro1237Ser",
"transcript": "NM_005633.4",
"protein_id": "NP_005624.2",
"transcript_support_level": null,
"aa_start": 1237,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3709,
"cds_end": null,
"cds_length": 4002,
"cdna_start": 4338,
"cdna_end": null,
"cdna_length": 8906,
"mane_select": "ENST00000402219.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3709C>T",
"hgvs_p": "p.Pro1237Ser",
"transcript": "ENST00000402219.8",
"protein_id": "ENSP00000384675.2",
"transcript_support_level": 1,
"aa_start": 1237,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3709,
"cds_end": null,
"cds_length": 4002,
"cdna_start": 4338,
"cdna_end": null,
"cdna_length": 8906,
"mane_select": "NM_005633.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3688C>T",
"hgvs_p": "p.Pro1230Ser",
"transcript": "NM_001382394.1",
"protein_id": "NP_001369323.1",
"transcript_support_level": null,
"aa_start": 1230,
"aa_end": null,
"aa_length": 1326,
"cds_start": 3688,
"cds_end": null,
"cds_length": 3981,
"cdna_start": 3827,
"cdna_end": null,
"cdna_length": 8395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3664C>T",
"hgvs_p": "p.Pro1222Ser",
"transcript": "NM_001382395.1",
"protein_id": "NP_001369324.1",
"transcript_support_level": null,
"aa_start": 1222,
"aa_end": null,
"aa_length": 1318,
"cds_start": 3664,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 4293,
"cdna_end": null,
"cdna_length": 8861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3664C>T",
"hgvs_p": "p.Pro1222Ser",
"transcript": "ENST00000395038.6",
"protein_id": "ENSP00000378479.2",
"transcript_support_level": 5,
"aa_start": 1222,
"aa_end": null,
"aa_length": 1318,
"cds_start": 3664,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 3692,
"cdna_end": null,
"cdna_length": 4123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.2476C>T",
"hgvs_p": "p.Pro826Ser",
"transcript": "ENST00000685279.1",
"protein_id": "ENSP00000509424.1",
"transcript_support_level": null,
"aa_start": 826,
"aa_end": null,
"aa_length": 922,
"cds_start": 2476,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 2543,
"cdna_end": null,
"cdna_length": 7030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3643C>T",
"hgvs_p": "p.Pro1215Ser",
"transcript": "XM_047445581.1",
"protein_id": "XP_047301537.1",
"transcript_support_level": null,
"aa_start": 1215,
"aa_end": null,
"aa_length": 1311,
"cds_start": 3643,
"cds_end": null,
"cds_length": 3936,
"cdna_start": 3782,
"cdna_end": null,
"cdna_length": 8350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3538C>T",
"hgvs_p": "p.Pro1180Ser",
"transcript": "XM_011533064.3",
"protein_id": "XP_011531366.1",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3538,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 7298,
"cdna_end": null,
"cdna_length": 11866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3538C>T",
"hgvs_p": "p.Pro1180Ser",
"transcript": "XM_047445582.1",
"protein_id": "XP_047301538.1",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3538,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 3928,
"cdna_end": null,
"cdna_length": 8496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.2644C>T",
"hgvs_p": "p.Pro882Ser",
"transcript": "XM_047445585.1",
"protein_id": "XP_047301541.1",
"transcript_support_level": null,
"aa_start": 882,
"aa_end": null,
"aa_length": 978,
"cds_start": 2644,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 2659,
"cdna_end": null,
"cdna_length": 7227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1570C>T",
"hgvs_p": "p.Pro524Ser",
"transcript": "XM_047445586.1",
"protein_id": "XP_047301542.1",
"transcript_support_level": null,
"aa_start": 524,
"aa_end": null,
"aa_length": 620,
"cds_start": 1570,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 1853,
"cdna_end": null,
"cdna_length": 6421,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.452C>T",
"hgvs_p": null,
"transcript": "ENST00000469581.1",
"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": 523,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.500C>T",
"hgvs_p": null,
"transcript": "ENST00000686849.1",
"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": 2761,
"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": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.*1015C>T",
"hgvs_p": null,
"transcript": "ENST00000690876.1",
"protein_id": "ENSP00000508955.1",
"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": 5987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.*1015C>T",
"hgvs_p": null,
"transcript": "ENST00000690876.1",
"protein_id": "ENSP00000508955.1",
"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": 5987,
"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": 22,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3399+1356C>T",
"hgvs_p": null,
"transcript": "ENST00000692089.1",
"protein_id": "ENSP00000508626.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1147,
"cds_start": -4,
"cds_end": null,
"cds_length": 3444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4056,
"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": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1162-754C>T",
"hgvs_p": null,
"transcript": "ENST00000692227.1",
"protein_id": "ENSP00000509138.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 404,
"cds_start": -4,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1735,
"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": 23,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3511-754C>T",
"hgvs_p": null,
"transcript": "XM_047445583.1",
"protein_id": "XP_047301539.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1187,
"cds_start": -4,
"cds_end": null,
"cds_length": 3564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7951,
"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": 22,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.3466-754C>T",
"hgvs_p": null,
"transcript": "XM_047445584.1",
"protein_id": "XP_047301540.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1172,
"cds_start": -4,
"cds_end": null,
"cds_length": 3519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"dbsnp": "rs371408734",
"frequency_reference_population": 0.00001026215,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.0000102622,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3358510434627533,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.439,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.114,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.812,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005633.4",
"gene_symbol": "SOS1",
"hgnc_id": 11187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3709C>T",
"hgvs_p": "p.Pro1237Ser"
}
],
"clinvar_disease": " 1, gingival,Cardiovascular phenotype,Fibromatosis,Noonan syndrome 4,RASopathy,SOS1-related disorder,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6",
"phenotype_combined": "not provided|RASopathy|Cardiovascular phenotype|Fibromatosis, gingival, 1|Noonan syndrome 4|SOS1-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}