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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: 21-25599810-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=25599810&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"PP2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MRPL39",
"hgnc_id": 14027,
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 1,
"transcript": "NM_080794.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,BP4_Moderate",
"acmg_score": 1,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.0833,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"chr": "21",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09505462646484375,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 338,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1074,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1017,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_017446.4",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000352957.9",
"protein_coding": true,
"protein_id": "NP_059142.3",
"strand": false,
"transcript": "NM_017446.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 338,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1074,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1017,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000352957.9",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017446.4",
"protein_coding": true,
"protein_id": "ENSP00000284967.7",
"strand": false,
"transcript": "ENST00000352957.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 353,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1163,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1062,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_080794.4",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542984.3",
"strand": false,
"transcript": "NM_080794.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 353,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1199,
"cdna_start": 619,
"cds_end": null,
"cds_length": 1062,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000307301.11",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000305682.7",
"strand": false,
"transcript": "ENST00000307301.11",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 344,
"aa_ref": "M",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1092,
"cdna_start": 601,
"cds_end": null,
"cds_length": 1035,
"cds_start": 595,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925346.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.595A>T",
"hgvs_p": "p.Met199Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595405.1",
"strand": false,
"transcript": "ENST00000925346.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 339,
"aa_ref": "M",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1124,
"cdna_start": 630,
"cds_end": null,
"cds_length": 1020,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925341.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.580A>T",
"hgvs_p": "p.Met194Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595400.1",
"strand": false,
"transcript": "ENST00000925341.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 337,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1079,
"cdna_start": 594,
"cds_end": null,
"cds_length": 1014,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000946900.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616959.1",
"strand": false,
"transcript": "ENST00000946900.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 325,
"aa_ref": "M",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1035,
"cdna_start": 544,
"cds_end": null,
"cds_length": 978,
"cds_start": 538,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925344.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.538A>T",
"hgvs_p": "p.Met180Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595403.1",
"strand": false,
"transcript": "ENST00000925344.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 323,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1029,
"cdna_start": 583,
"cds_end": null,
"cds_length": 972,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000946901.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616960.1",
"strand": false,
"transcript": "ENST00000946901.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 322,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1090,
"cdna_start": 623,
"cds_end": null,
"cds_length": 969,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925340.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595399.1",
"strand": false,
"transcript": "ENST00000925340.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 321,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1015,
"cdna_start": 583,
"cds_end": null,
"cds_length": 966,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000875588.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545647.1",
"strand": false,
"transcript": "ENST00000875588.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "M",
"aa_start": 175,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1012,
"cdna_start": 529,
"cds_end": null,
"cds_length": 963,
"cds_start": 523,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000875589.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.523A>T",
"hgvs_p": "p.Met175Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545648.1",
"strand": false,
"transcript": "ENST00000875589.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 300,
"aa_ref": "M",
"aa_start": 155,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 979,
"cdna_start": 488,
"cds_end": null,
"cds_length": 903,
"cds_start": 463,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925343.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.463A>T",
"hgvs_p": "p.Met155Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595402.1",
"strand": false,
"transcript": "ENST00000925343.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 296,
"aa_ref": "M",
"aa_start": 183,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 900,
"cdna_start": 556,
"cds_end": null,
"cds_length": 891,
"cds_start": 547,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000419219.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.547A>T",
"hgvs_p": "p.Met183Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000404426.1",
"strand": false,
"transcript": "ENST00000419219.1",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 269,
"aa_ref": "M",
"aa_start": 124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 867,
"cdna_start": 376,
"cds_end": null,
"cds_length": 810,
"cds_start": 370,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000925345.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Met124Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595404.1",
"strand": false,
"transcript": "ENST00000925345.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 258,
"aa_ref": "M",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 858,
"cdna_start": 367,
"cds_end": null,
"cds_length": 777,
"cds_start": 337,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000925342.1",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.337A>T",
"hgvs_p": "p.Met113Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595401.1",
"strand": false,
"transcript": "ENST00000925342.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 353,
"aa_ref": "M",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1155,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1062,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_006724026.5",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.577A>T",
"hgvs_p": "p.Met193Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724089.1",
"strand": false,
"transcript": "XM_006724026.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 296,
"aa_ref": "M",
"aa_start": 151,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1154,
"cdna_start": 663,
"cds_end": null,
"cds_length": 891,
"cds_start": 451,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011529651.3",
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"hgvs_c": "c.451A>T",
"hgvs_p": "p.Met151Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527953.1",
"strand": false,
"transcript": "XM_011529651.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs763280524",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013698311,
"gene_hgnc_id": 14027,
"gene_symbol": "MRPL39",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136983,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.552,
"pos": 25599810,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.033,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_080794.4"
}
]
}