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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: 2-39023128-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=39023128&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 39023128,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000402219.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "NM_005633.4",
"protein_id": "NP_005624.2",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 1333,
"cds_start": 1300,
"cds_end": null,
"cds_length": 4002,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 8906,
"mane_select": "ENST00000402219.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "ENST00000402219.8",
"protein_id": "ENSP00000384675.2",
"transcript_support_level": 1,
"aa_start": 434,
"aa_end": null,
"aa_length": 1333,
"cds_start": 1300,
"cds_end": null,
"cds_length": 4002,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 8906,
"mane_select": "NM_005633.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1279G>A",
"hgvs_p": "p.Gly427Arg",
"transcript": "NM_001382394.1",
"protein_id": "NP_001369323.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1326,
"cds_start": 1279,
"cds_end": null,
"cds_length": 3981,
"cdna_start": 1418,
"cdna_end": null,
"cdna_length": 8395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "NM_001382395.1",
"protein_id": "NP_001369324.1",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 1318,
"cds_start": 1300,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 8861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "ENST00000395038.6",
"protein_id": "ENSP00000378479.2",
"transcript_support_level": 5,
"aa_start": 434,
"aa_end": null,
"aa_length": 1318,
"cds_start": 1300,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 1328,
"cdna_end": null,
"cdna_length": 4123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1189G>A",
"hgvs_p": "p.Gly397Arg",
"transcript": "ENST00000692089.1",
"protein_id": "ENSP00000508626.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 1147,
"cds_start": 1189,
"cds_end": null,
"cds_length": 3444,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 4056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1189G>A",
"hgvs_p": "p.Gly397Arg",
"transcript": "ENST00000691229.1",
"protein_id": "ENSP00000510437.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1189,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 5976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.67G>A",
"hgvs_p": "p.Gly23Arg",
"transcript": "ENST00000685279.1",
"protein_id": "ENSP00000509424.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 922,
"cds_start": 67,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 7030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1279G>A",
"hgvs_p": "p.Gly427Arg",
"transcript": "XM_047445581.1",
"protein_id": "XP_047301537.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1311,
"cds_start": 1279,
"cds_end": null,
"cds_length": 3936,
"cdna_start": 1418,
"cdna_end": null,
"cdna_length": 8350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1129G>A",
"hgvs_p": "p.Gly377Arg",
"transcript": "XM_011533064.3",
"protein_id": "XP_011531366.1",
"transcript_support_level": null,
"aa_start": 377,
"aa_end": null,
"aa_length": 1276,
"cds_start": 1129,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 4889,
"cdna_end": null,
"cdna_length": 11866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1129G>A",
"hgvs_p": "p.Gly377Arg",
"transcript": "XM_047445582.1",
"protein_id": "XP_047301538.1",
"transcript_support_level": null,
"aa_start": 377,
"aa_end": null,
"aa_length": 1276,
"cds_start": 1129,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 8496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "XM_047445583.1",
"protein_id": "XP_047301539.1",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 1187,
"cds_start": 1300,
"cds_end": null,
"cds_length": 3564,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 7951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg",
"transcript": "XM_047445584.1",
"protein_id": "XP_047301540.1",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 1172,
"cds_start": 1300,
"cds_end": null,
"cds_length": 3519,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 7906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "c.235G>A",
"hgvs_p": "p.Gly79Arg",
"transcript": "XM_047445585.1",
"protein_id": "XP_047301541.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 978,
"cds_start": 235,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 7227,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.1180G>A",
"hgvs_p": null,
"transcript": "ENST00000472480.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 4370,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.1521G>A",
"hgvs_p": null,
"transcript": "ENST00000688043.1",
"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": 4898,
"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": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.1307G>A",
"hgvs_p": null,
"transcript": "ENST00000689668.1",
"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": 3407,
"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": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.1189G>A",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.67G>A",
"hgvs_p": null,
"transcript": "ENST00000692620.1",
"protein_id": "ENSP00000509311.1",
"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": 4772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"hgvs_c": "n.*271G>A",
"hgvs_p": null,
"transcript": "ENST00000690679.1",
"protein_id": "ENSP00000509380.1",
"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": 1469,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SOS1",
"gene_hgnc_id": 11187,
"dbsnp": "rs397517148",
"frequency_reference_population": 6.8436805e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84368e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9690762758255005,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.927,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9995,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.795,
"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": 26,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1_Very_Strong,PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 26,
"benign_score": 0,
"pathogenic_score": 26,
"criteria": [
"PS1_Very_Strong",
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000402219.8",
"gene_symbol": "SOS1",
"hgnc_id": 11187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1300G>A",
"hgvs_p": "p.Gly434Arg"
}
],
"clinvar_disease": " 1, gingival,Abnormal sternum morphology,Cardiovascular phenotype,Fetal cystic hygroma,Fibromatosis,Noonan syndrome,Noonan syndrome 1,Noonan syndrome 4,Noonan syndrome and Noonan-related syndrome,Ptosis,Pulmonic stenosis,RASopathy,Short stature,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:12 LP:2",
"phenotype_combined": "Noonan syndrome|Fetal cystic hygroma|Noonan syndrome and Noonan-related syndrome|Fibromatosis, gingival, 1;Noonan syndrome 4|Cardiovascular phenotype|Pulmonic stenosis;Ptosis;Abnormal sternum morphology;Short stature|not provided|RASopathy|Noonan syndrome 1|Noonan syndrome 4",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}