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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: 10-100749759-T-TGTGAACC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=100749759&ref=T&alt=TGTGAACC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 100749759,
"ref": "T",
"alt": "TGTGAACC",
"effect": "frameshift_variant",
"transcript": "ENST00000355243.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "NM_000278.5",
"protein_id": "NP_000269.3",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 394,
"cds_start": 65,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": "ENST00000355243.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "ENST00000355243.8",
"protein_id": "ENSP00000347385.3",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 394,
"cds_start": 65,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": "NM_000278.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "ENST00000370296.6",
"protein_id": "ENSP00000359319.3",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 396,
"cds_start": 65,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 615,
"cdna_end": null,
"cdna_length": 4140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.70_76dupGTGAACC",
"hgvs_p": "p.Gln26fs",
"transcript": "ENST00000554172.2",
"protein_id": "ENSP00000452489.2",
"transcript_support_level": 1,
"aa_start": 26,
"aa_end": null,
"aa_length": 303,
"cds_start": 77,
"cds_end": null,
"cds_length": 914,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "NM_003990.5",
"protein_id": "NP_003981.3",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 432,
"cds_start": 65,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "ENST00000707079.1",
"protein_id": "ENSP00000516730.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 432,
"cds_start": 65,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.151_157dupGTGAACC",
"hgvs_p": "p.Gln53fs",
"transcript": "NM_001304569.2",
"protein_id": "NP_001291498.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 425,
"cds_start": 158,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 3916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.151_157dupGTGAACC",
"hgvs_p": "p.Gln53fs",
"transcript": "ENST00000707078.1",
"protein_id": "ENSP00000516729.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 425,
"cds_start": 158,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 3916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "NM_003987.5",
"protein_id": "NP_003978.3",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 417,
"cds_start": 65,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "ENST00000428433.5",
"protein_id": "ENSP00000396259.1",
"transcript_support_level": 5,
"aa_start": 22,
"aa_end": null,
"aa_length": 417,
"cds_start": 65,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 615,
"cdna_end": null,
"cdna_length": 4126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "NM_003989.5",
"protein_id": "NP_003980.3",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 409,
"cds_start": 65,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "ENST00000427256.6",
"protein_id": "ENSP00000398652.2",
"transcript_support_level": 3,
"aa_start": 22,
"aa_end": null,
"aa_length": 409,
"cds_start": 65,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs",
"transcript": "NM_003988.5",
"protein_id": "NP_003979.2",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 396,
"cds_start": 65,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.55_61dupGTGAACC",
"hgvs_p": "p.Gln21fs",
"transcript": "ENST00000361791.7",
"protein_id": "ENSP00000355069.4",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 393,
"cds_start": 62,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 103,
"cdna_end": null,
"cdna_length": 3193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "REP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "c.40_46dupGTGAACC",
"hgvs_p": "p.Gln16fs",
"transcript": "ENST00000679374.1",
"protein_id": "ENSP00000506041.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 388,
"cds_start": 47,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 3805,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "n.1060_1066dupGTGAACC",
"hgvs_p": null,
"transcript": "ENST00000483202.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 1216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "n.131+14027_131+14033dupGTGAACC",
"hgvs_p": null,
"transcript": "ENST00000553492.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"hgvs_c": "n.125+3457_125+3463dupGTGAACC",
"hgvs_p": null,
"transcript": "ENST00000554363.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PAX2",
"gene_hgnc_id": 8616,
"dbsnp": "rs886037756",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.996,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000355243.8",
"gene_symbol": "PAX2",
"hgnc_id": 8616,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.58_64dupGTGAACC",
"hgvs_p": "p.Gln22fs"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}