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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: 7-116778956-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116778956&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 116778956,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001127500.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3521A>G",
"hgvs_p": "p.His1174Arg",
"transcript": "NM_000245.4",
"protein_id": "NP_000236.2",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 1390,
"cds_start": 3521,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 3917,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "ENST00000397752.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000245.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3521A>G",
"hgvs_p": "p.His1174Arg",
"transcript": "ENST00000397752.8",
"protein_id": "ENSP00000380860.3",
"transcript_support_level": 1,
"aa_start": 1174,
"aa_end": null,
"aa_length": 1390,
"cds_start": 3521,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 3917,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "NM_000245.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397752.8"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3575A>G",
"hgvs_p": "p.His1192Arg",
"transcript": "ENST00000318493.11",
"protein_id": "ENSP00000317272.6",
"transcript_support_level": 1,
"aa_start": 1192,
"aa_end": null,
"aa_length": 1408,
"cds_start": 3575,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 3971,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000318493.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*1126A>G",
"hgvs_p": null,
"transcript": "ENST00000436117.3",
"protein_id": "ENSP00000410980.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6722,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000436117.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*1126A>G",
"hgvs_p": null,
"transcript": "ENST00000436117.3",
"protein_id": "ENSP00000410980.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6722,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000436117.3"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3575A>G",
"hgvs_p": "p.His1192Arg",
"transcript": "NM_001127500.3",
"protein_id": "NP_001120972.1",
"transcript_support_level": null,
"aa_start": 1192,
"aa_end": null,
"aa_length": 1408,
"cds_start": 3575,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 3971,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127500.3"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3518A>G",
"hgvs_p": "p.His1173Arg",
"transcript": "ENST00000950406.1",
"protein_id": "ENSP00000620465.1",
"transcript_support_level": null,
"aa_start": 1173,
"aa_end": null,
"aa_length": 1389,
"cds_start": 3518,
"cds_end": null,
"cds_length": 4170,
"cdna_start": 4059,
"cdna_end": null,
"cdna_length": 6962,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950406.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3437A>G",
"hgvs_p": "p.His1146Arg",
"transcript": "ENST00000917365.1",
"protein_id": "ENSP00000587424.1",
"transcript_support_level": null,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3437,
"cds_end": null,
"cds_length": 4089,
"cdna_start": 3744,
"cdna_end": null,
"cdna_length": 6658,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917365.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3521A>G",
"hgvs_p": "p.His1174Arg",
"transcript": "ENST00000950407.1",
"protein_id": "ENSP00000620466.1",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 1298,
"cds_start": 3521,
"cds_end": null,
"cds_length": 3897,
"cdna_start": 3957,
"cdna_end": null,
"cdna_length": 6582,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950407.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2231A>G",
"hgvs_p": "p.His744Arg",
"transcript": "NM_001324402.2",
"protein_id": "NP_001311331.1",
"transcript_support_level": null,
"aa_start": 744,
"aa_end": null,
"aa_length": 960,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 2703,
"cdna_end": null,
"cdna_length": 5608,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001324402.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3578A>G",
"hgvs_p": "p.His1193Arg",
"transcript": "XM_011516223.2",
"protein_id": "XP_011514525.1",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1409,
"cds_start": 3578,
"cds_end": null,
"cds_length": 4230,
"cdna_start": 3967,
"cdna_end": null,
"cdna_length": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011516223.2"
}
],
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"dbsnp": "rs372830789",
"frequency_reference_population": 0.000071885646,
"hom_count_reference_population": 0,
"allele_count_reference_population": 116,
"gnomad_exomes_af": 0.0000424273,
"gnomad_genomes_af": 0.000354442,
"gnomad_exomes_ac": 62,
"gnomad_genomes_ac": 54,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08867776393890381,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.5320000052452087,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.389,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3317,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.275,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.498338907529119,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001127500.3",
"gene_symbol": "MET",
"hgnc_id": 7029,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.3575A>G",
"hgvs_p": "p.His1192Arg"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,MET-related disorder,Renal cell carcinoma,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Renal cell carcinoma|Hereditary cancer-predisposing syndrome|not provided|not specified|MET-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}