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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: 12-112502222-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112502222&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112502222,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000351677.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1678C>T",
"hgvs_p": "p.Leu560Phe",
"transcript": "NM_002834.5",
"protein_id": "NP_002825.3",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 593,
"cds_start": 1678,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1843,
"cdna_end": null,
"cdna_length": 6073,
"mane_select": "ENST00000351677.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1678C>T",
"hgvs_p": "p.Leu560Phe",
"transcript": "ENST00000351677.7",
"protein_id": "ENSP00000340944.3",
"transcript_support_level": 1,
"aa_start": 560,
"aa_end": null,
"aa_length": 593,
"cds_start": 1678,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1843,
"cdna_end": null,
"cdna_length": 6073,
"mane_select": "NM_002834.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Leu564Phe",
"transcript": "ENST00000635625.1",
"protein_id": "ENSP00000489597.1",
"transcript_support_level": 5,
"aa_start": 564,
"aa_end": null,
"aa_length": 597,
"cds_start": 1690,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1690,
"cdna_end": null,
"cdna_length": 1794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1678C>T",
"hgvs_p": "p.Leu560Phe",
"transcript": "ENST00000690210.1",
"protein_id": "ENSP00000509272.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 671,
"cds_start": 1678,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1883,
"cdna_end": null,
"cdna_length": 6274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Leu564Phe",
"transcript": "NM_001330437.2",
"protein_id": "NP_001317366.1",
"transcript_support_level": null,
"aa_start": 564,
"aa_end": null,
"aa_length": 597,
"cds_start": 1690,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 6085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1675C>T",
"hgvs_p": "p.Leu559Phe",
"transcript": "NM_001374625.1",
"protein_id": "NP_001361554.1",
"transcript_support_level": null,
"aa_start": 559,
"aa_end": null,
"aa_length": 592,
"cds_start": 1675,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1840,
"cdna_end": null,
"cdna_length": 6070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1678C>T",
"hgvs_p": "p.Leu560Phe",
"transcript": "ENST00000639857.2",
"protein_id": "ENSP00000491593.2",
"transcript_support_level": 5,
"aa_start": 560,
"aa_end": null,
"aa_length": 578,
"cds_start": 1678,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 1883,
"cdna_end": null,
"cdna_length": 4455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1564C>T",
"hgvs_p": "p.Leu522Phe",
"transcript": "ENST00000687906.1",
"protein_id": "ENSP00000509536.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 555,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1765,
"cdna_end": null,
"cdna_length": 5995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1303C>T",
"hgvs_p": "p.Leu435Phe",
"transcript": "ENST00000688597.1",
"protein_id": "ENSP00000510628.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 468,
"cds_start": 1303,
"cds_end": null,
"cds_length": 1407,
"cdna_start": 1508,
"cdna_end": null,
"cdna_length": 5738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1687C>T",
"hgvs_p": "p.Leu563Phe",
"transcript": "XM_011538613.3",
"protein_id": "XP_011536915.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 596,
"cds_start": 1687,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 6082,
"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": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.*880C>T",
"hgvs_p": null,
"transcript": "ENST00000685487.1",
"protein_id": "ENSP00000508503.1",
"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": 6926,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.1061C>T",
"hgvs_p": null,
"transcript": "ENST00000687120.1",
"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": 7648,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.922C>T",
"hgvs_p": null,
"transcript": "ENST00000688701.1",
"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": 5152,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.887C>T",
"hgvs_p": null,
"transcript": "ENST00000690472.1",
"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": 5117,
"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": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.*224C>T",
"hgvs_p": null,
"transcript": "ENST00000692624.1",
"protein_id": "ENSP00000508953.1",
"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": 6045,
"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": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.*880C>T",
"hgvs_p": null,
"transcript": "ENST00000685487.1",
"protein_id": "ENSP00000508503.1",
"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": 6926,
"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": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.*224C>T",
"hgvs_p": null,
"transcript": "ENST00000692624.1",
"protein_id": "ENSP00000508953.1",
"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": 6045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"dbsnp": "rs397516797",
"frequency_reference_population": 0.00004833528,
"hom_count_reference_population": 0,
"allele_count_reference_population": 78,
"gnomad_exomes_af": 0.0000458415,
"gnomad_genomes_af": 0.0000722876,
"gnomad_exomes_ac": 67,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06261109560728073,
"computational_prediction_selected": "Benign",
"computational_source_selected": "CardioboostCm",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.206,
"revel_prediction": "Benign",
"alphamissense_score": 0.1257,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.487,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": "BP5,BS3",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP5",
"BS3"
],
"verdict": "Likely_benign",
"transcript": "ENST00000351677.7",
"gene_symbol": "PTPN11",
"hgnc_id": 9644,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1678C>T",
"hgvs_p": "p.Leu560Phe"
}
],
"clinvar_disease": "Cardiovascular phenotype,Juvenile myelomonocytic leukemia,LEOPARD syndrome 1,Metachondromatosis,Noonan syndrome 1,Noonan syndrome and Noonan-related syndrome,PTPN11-related disorder,RASopathy,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:5 LB:4",
"phenotype_combined": "not specified|not provided|RASopathy|Noonan syndrome 1;Juvenile myelomonocytic leukemia;LEOPARD syndrome 1;Metachondromatosis|Metachondromatosis|Noonan syndrome and Noonan-related syndrome|Cardiovascular phenotype|PTPN11-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}