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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: 12-70540937-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=70540937&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PTPRB",
"hgnc_id": 9665,
"hgvs_c": "c.5515G>C",
"hgvs_p": "p.Glu1839Gln",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_001109754.4",
"verdict": "Likely_benign"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PTPRB-AS1",
"hgnc_id": 58150,
"hgvs_c": "n.3800C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000548687.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 64,
"alphamissense_prediction": null,
"alphamissense_score": 0.3125,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"chr": "12",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.47713804244995117,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2215,
"aa_ref": "E",
"aa_start": 1839,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12301,
"cdna_start": 5549,
"cds_end": null,
"cds_length": 6648,
"cds_start": 5515,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_001109754.4",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5515G>C",
"hgvs_p": "p.Glu1839Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000334414.11",
"protein_coding": true,
"protein_id": "NP_001103224.1",
"strand": false,
"transcript": "NM_001109754.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2215,
"aa_ref": "E",
"aa_start": 1839,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 12301,
"cdna_start": 5549,
"cds_end": null,
"cds_length": 6648,
"cds_start": 5515,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000334414.11",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5515G>C",
"hgvs_p": "p.Glu1839Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001109754.4",
"protein_coding": true,
"protein_id": "ENSP00000334928.6",
"strand": false,
"transcript": "ENST00000334414.11",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1997,
"aa_ref": "E",
"aa_start": 1621,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6110,
"cdna_start": 4891,
"cds_end": null,
"cds_length": 5994,
"cds_start": 4861,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000261266.9",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4861G>C",
"hgvs_p": "p.Glu1621Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000261266.5",
"strand": false,
"transcript": "ENST00000261266.9",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1907,
"aa_ref": "E",
"aa_start": 1531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5839,
"cdna_start": 4620,
"cds_end": null,
"cds_length": 5724,
"cds_start": 4591,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000538708.5",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4591G>C",
"hgvs_p": "p.Glu1531Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000438927.1",
"strand": false,
"transcript": "ENST00000538708.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1907,
"aa_ref": "E",
"aa_start": 1531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5839,
"cdna_start": 4620,
"cds_end": null,
"cds_length": 5724,
"cds_start": 4591,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000550857.5",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4591G>C",
"hgvs_p": "p.Glu1531Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000447302.1",
"strand": false,
"transcript": "ENST00000550857.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5903,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000548687.5",
"gene_hgnc_id": 58150,
"gene_symbol": "PTPRB-AS1",
"hgvs_c": "n.3800C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000548687.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2127,
"aa_ref": "E",
"aa_start": 1751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12037,
"cdna_start": 5285,
"cds_end": null,
"cds_length": 6384,
"cds_start": 5251,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_001330204.2",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5251G>C",
"hgvs_p": "p.Glu1751Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317133.1",
"strand": false,
"transcript": "NM_001330204.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2127,
"aa_ref": "E",
"aa_start": 1751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6583,
"cdna_start": 5277,
"cds_end": null,
"cds_length": 6384,
"cds_start": 5251,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000550358.5",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5251G>C",
"hgvs_p": "p.Glu1751Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000448058.1",
"strand": false,
"transcript": "ENST00000550358.5",
"transcript_support_level": 2
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2125,
"aa_ref": "E",
"aa_start": 1749,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6483,
"cdna_start": 5280,
"cds_end": null,
"cds_length": 6378,
"cds_start": 5245,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000952654.1",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5245G>C",
"hgvs_p": "p.Glu1749Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622713.1",
"strand": false,
"transcript": "ENST00000952654.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1997,
"aa_ref": "E",
"aa_start": 1621,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11823,
"cdna_start": 5071,
"cds_end": null,
"cds_length": 5994,
"cds_start": 4861,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_002837.6",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4861G>C",
"hgvs_p": "p.Glu1621Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_002828.3",
"strand": false,
"transcript": "NM_002837.6",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1907,
"aa_ref": "E",
"aa_start": 1531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11553,
"cdna_start": 4801,
"cds_end": null,
"cds_length": 5724,
"cds_start": 4591,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001206971.3",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4591G>C",
"hgvs_p": "p.Glu1531Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193900.1",
"strand": false,
"transcript": "NM_001206971.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1907,
"aa_ref": "E",
"aa_start": 1531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11553,
"cdna_start": 4801,
"cds_end": null,
"cds_length": 5724,
"cds_start": 4591,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001206972.3",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4591G>C",
"hgvs_p": "p.Glu1531Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193901.1",
"strand": false,
"transcript": "NM_001206972.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2230,
"aa_ref": "E",
"aa_start": 1839,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6841,
"cdna_start": 5549,
"cds_end": null,
"cds_length": 6693,
"cds_start": 5515,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_006719528.2",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5515G>C",
"hgvs_p": "p.Glu1839Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006719591.1",
"strand": false,
"transcript": "XM_006719528.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2142,
"aa_ref": "E",
"aa_start": 1751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6577,
"cdna_start": 5285,
"cds_end": null,
"cds_length": 6429,
"cds_start": 5251,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011538614.2",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.5251G>C",
"hgvs_p": "p.Glu1751Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536916.1",
"strand": false,
"transcript": "XM_011538614.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 2012,
"aa_ref": "E",
"aa_start": 1621,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6363,
"cdna_start": 5071,
"cds_end": null,
"cds_length": 6039,
"cds_start": 4861,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_006719529.5",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.4861G>C",
"hgvs_p": "p.Glu1621Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006719592.1",
"strand": false,
"transcript": "XM_006719529.5",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1446,
"aa_ref": "E",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4627,
"cdna_start": 3335,
"cds_end": null,
"cds_length": 4341,
"cds_start": 3163,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_017019724.1",
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"hgvs_c": "c.3163G>C",
"hgvs_p": "p.Glu1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016875213.1",
"strand": false,
"transcript": "XM_017019724.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4387,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000667308.1",
"gene_hgnc_id": 58150,
"gene_symbol": "PTPRB-AS1",
"hgvs_c": "n.3409C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000667308.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 14931,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XR_007063360.1",
"gene_hgnc_id": 58150,
"gene_symbol": "PTPRB-AS1",
"hgvs_c": "n.12827C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007063360.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 12450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001749196.2",
"gene_hgnc_id": 58150,
"gene_symbol": "PTPRB-AS1",
"hgvs_c": "n.10006+13199C>G",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001749196.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376983206",
"effect": "missense_variant",
"frequency_reference_population": 0.000039885777,
"gene_hgnc_id": 9665,
"gene_symbol": "PTPRB",
"gnomad_exomes_ac": 54,
"gnomad_exomes_af": 0.0000371796,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.0000657151,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.762,
"pos": 70540937,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.287,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10000000149011612,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.1,
"transcript": "NM_001109754.4"
}
]
}