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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: 7-116774970-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116774970&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 116774970,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001127500.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3118T>C",
"hgvs_p": "p.Ser1040Pro",
"transcript": "NM_000245.4",
"protein_id": "NP_000236.2",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1390,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000397752.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000245.4"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3118T>C",
"hgvs_p": "p.Ser1040Pro",
"transcript": "ENST00000397752.8",
"protein_id": "ENSP00000380860.3",
"transcript_support_level": 1,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1390,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000245.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397752.8"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3172T>C",
"hgvs_p": "p.Ser1058Pro",
"transcript": "ENST00000318493.11",
"protein_id": "ENSP00000317272.6",
"transcript_support_level": 1,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1408,
"cds_start": 3172,
"cds_end": null,
"cds_length": 4227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*723T>C",
"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": null,
"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": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*723T>C",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000436117.3"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3172T>C",
"hgvs_p": "p.Ser1058Pro",
"transcript": "NM_001127500.3",
"protein_id": "NP_001120972.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1408,
"cds_start": 3172,
"cds_end": null,
"cds_length": 4227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127500.3"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3115T>C",
"hgvs_p": "p.Ser1039Pro",
"transcript": "ENST00000950406.1",
"protein_id": "ENSP00000620465.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1389,
"cds_start": 3115,
"cds_end": null,
"cds_length": 4170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950406.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3034T>C",
"hgvs_p": "p.Ser1012Pro",
"transcript": "ENST00000917365.1",
"protein_id": "ENSP00000587424.1",
"transcript_support_level": null,
"aa_start": 1012,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3034,
"cds_end": null,
"cds_length": 4089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917365.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3118T>C",
"hgvs_p": "p.Ser1040Pro",
"transcript": "ENST00000950407.1",
"protein_id": "ENSP00000620466.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1298,
"cds_start": 3118,
"cds_end": null,
"cds_length": 3897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950407.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1828T>C",
"hgvs_p": "p.Ser610Pro",
"transcript": "NM_001324402.2",
"protein_id": "NP_001311331.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 960,
"cds_start": 1828,
"cds_end": null,
"cds_length": 2883,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001324402.2"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.373T>C",
"hgvs_p": "p.Ser125Pro",
"transcript": "ENST00000454623.1",
"protein_id": "ENSP00000398140.1",
"transcript_support_level": 5,
"aa_start": 125,
"aa_end": null,
"aa_length": 157,
"cds_start": 373,
"cds_end": null,
"cds_length": 475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454623.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.3175T>C",
"hgvs_p": "p.Ser1059Pro",
"transcript": "XM_011516223.2",
"protein_id": "XP_011514525.1",
"transcript_support_level": null,
"aa_start": 1059,
"aa_end": null,
"aa_length": 1409,
"cds_start": 3175,
"cds_end": null,
"cds_length": 4230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011516223.2"
}
],
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"dbsnp": "rs771328219",
"frequency_reference_population": 0.000056380053,
"hom_count_reference_population": 0,
"allele_count_reference_population": 91,
"gnomad_exomes_af": 0.0000581463,
"gnomad_genomes_af": 0.0000394177,
"gnomad_exomes_ac": 85,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5302630662918091,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.407,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1859,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.013,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS1"
],
"verdict": "Likely_benign",
"transcript": "NM_001127500.3",
"gene_symbol": "MET",
"hgnc_id": 7029,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.3172T>C",
"hgvs_p": "p.Ser1058Pro"
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 97,Hereditary cancer-predisposing syndrome,Renal cell carcinoma,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "Renal cell carcinoma|Hereditary cancer-predisposing syndrome|not provided|Autosomal recessive nonsyndromic hearing loss 97",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}