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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: 19-49835774-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49835774&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49835774,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_001378355.1",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala",
"transcript": "NM_030973.4",
"protein_id": "NP_112235.2",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 747,
"cds_start": 1794,
"cds_end": null,
"cds_length": 2244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000312865.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030973.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala",
"transcript": "ENST00000312865.10",
"protein_id": "ENSP00000326767.5",
"transcript_support_level": 1,
"aa_start": 598,
"aa_end": null,
"aa_length": 747,
"cds_start": 1794,
"cds_end": null,
"cds_length": 2244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_030973.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000312865.10"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1155C>T",
"hgvs_p": "p.Ala385Ala",
"transcript": "ENST00000538643.5",
"protein_id": "ENSP00000437496.1",
"transcript_support_level": 1,
"aa_start": 385,
"aa_end": null,
"aa_length": 534,
"cds_start": 1155,
"cds_end": null,
"cds_length": 1605,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538643.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.689-1117C>T",
"hgvs_p": null,
"transcript": "ENST00000595185.5",
"protein_id": "ENSP00000470027.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 252,
"cds_start": null,
"cds_end": null,
"cds_length": 760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595185.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "n.2414C>T",
"hgvs_p": null,
"transcript": "ENST00000594998.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000594998.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1986C>T",
"hgvs_p": "p.Ala662Ala",
"transcript": "ENST00000929730.1",
"protein_id": "ENSP00000599789.1",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 811,
"cds_start": 1986,
"cds_end": null,
"cds_length": 2436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929730.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala",
"transcript": "NM_001378355.1",
"protein_id": "NP_001365284.1",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 796,
"cds_start": 1794,
"cds_end": null,
"cds_length": 2391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378355.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala",
"transcript": "ENST00000593767.3",
"protein_id": "ENSP00000470692.3",
"transcript_support_level": 3,
"aa_start": 598,
"aa_end": null,
"aa_length": 796,
"cds_start": 1794,
"cds_end": null,
"cds_length": 2391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593767.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1842C>T",
"hgvs_p": "p.Ala614Ala",
"transcript": "ENST00000929728.1",
"protein_id": "ENSP00000599787.1",
"transcript_support_level": null,
"aa_start": 614,
"aa_end": null,
"aa_length": 763,
"cds_start": 1842,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929728.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1824C>T",
"hgvs_p": "p.Ala608Ala",
"transcript": "ENST00000861903.1",
"protein_id": "ENSP00000531962.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 757,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2274,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861903.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala",
"transcript": "ENST00000861902.1",
"protein_id": "ENSP00000531961.1",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 745,
"cds_start": 1794,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861902.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1788C>T",
"hgvs_p": "p.Ala596Ala",
"transcript": "ENST00000929729.1",
"protein_id": "ENSP00000599788.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 745,
"cds_start": 1788,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929729.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1758C>T",
"hgvs_p": "p.Ala586Ala",
"transcript": "ENST00000861899.1",
"protein_id": "ENSP00000531958.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 735,
"cds_start": 1758,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861899.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1734C>T",
"hgvs_p": "p.Ala578Ala",
"transcript": "ENST00000861900.1",
"protein_id": "ENSP00000531959.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 727,
"cds_start": 1734,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861900.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1722C>T",
"hgvs_p": "p.Ala574Ala",
"transcript": "ENST00000861904.1",
"protein_id": "ENSP00000531963.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 723,
"cds_start": 1722,
"cds_end": null,
"cds_length": 2172,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861904.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1704C>T",
"hgvs_p": "p.Ala568Ala",
"transcript": "ENST00000861901.1",
"protein_id": "ENSP00000531960.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 717,
"cds_start": 1704,
"cds_end": null,
"cds_length": 2154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861901.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"hgvs_c": "c.1695C>T",
"hgvs_p": "p.Ala565Ala",
"transcript": "ENST00000861905.1",
"protein_id": "ENSP00000531964.1",
"transcript_support_level": null,
"aa_start": 565,
"aa_end": null,
"aa_length": 714,
"cds_start": 1695,
"cds_end": null,
"cds_length": 2145,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861905.1"
}
],
"gene_symbol": "MED25",
"gene_hgnc_id": 28845,
"dbsnp": "rs185100172",
"frequency_reference_population": 0.007566067,
"hom_count_reference_population": 89,
"allele_count_reference_population": 12173,
"gnomad_exomes_af": 0.00782982,
"gnomad_genomes_af": 0.00504321,
"gnomad_exomes_ac": 11405,
"gnomad_genomes_ac": 768,
"gnomad_exomes_homalt": 86,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.705,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001378355.1",
"gene_symbol": "MED25",
"hgnc_id": 28845,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Ala598Ala"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease type 2,Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Charcot-Marie-Tooth disease type 2|not specified|Charcot-Marie-Tooth disease|Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}