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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: 1-198742277-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=198742277&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 198742277,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000442510.8",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2607G>A",
"hgvs_p": "p.Met869Ile",
"transcript": "NM_002838.5",
"protein_id": "NP_002829.3",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2748,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "ENST00000442510.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2607G>A",
"hgvs_p": "p.Met869Ile",
"transcript": "ENST00000442510.8",
"protein_id": "ENSP00000411355.3",
"transcript_support_level": 1,
"aa_start": 869,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2748,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "NM_002838.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2124G>A",
"hgvs_p": "p.Met708Ile",
"transcript": "ENST00000348564.12",
"protein_id": "ENSP00000306782.7",
"transcript_support_level": 1,
"aa_start": 708,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2124,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2337,
"cdna_end": null,
"cdna_length": 6812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2322G>A",
"hgvs_p": "p.Met774Ile",
"transcript": "ENST00000697631.1",
"protein_id": "ENSP00000513363.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1211,
"cds_start": 2322,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 2408,
"cdna_end": null,
"cdna_length": 4699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2124G>A",
"hgvs_p": "p.Met708Ile",
"transcript": "NM_080921.4",
"protein_id": "NP_563578.2",
"transcript_support_level": null,
"aa_start": 708,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2124,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2265,
"cdna_end": null,
"cdna_length": 4874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Met523Ile",
"transcript": "ENST00000697632.1",
"protein_id": "ENSP00000513364.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 960,
"cds_start": 1569,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 2093,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2607G>A",
"hgvs_p": "p.Met869Ile",
"transcript": "XM_047426381.1",
"protein_id": "XP_047282337.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2724,
"cdna_end": null,
"cdna_length": 5333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2463G>A",
"hgvs_p": "p.Met821Ile",
"transcript": "XM_006711472.5",
"protein_id": "XP_006711535.1",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 1258,
"cds_start": 2463,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 2604,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2409G>A",
"hgvs_p": "p.Met803Ile",
"transcript": "XM_006711473.4",
"protein_id": "XP_006711536.1",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 1240,
"cds_start": 2409,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 2550,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2409G>A",
"hgvs_p": "p.Met803Ile",
"transcript": "XM_047426398.1",
"protein_id": "XP_047282354.1",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 1240,
"cds_start": 2409,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 2526,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2265G>A",
"hgvs_p": "p.Met755Ile",
"transcript": "XM_006711474.4",
"protein_id": "XP_006711537.1",
"transcript_support_level": null,
"aa_start": 755,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2265,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 2406,
"cdna_end": null,
"cdna_length": 5015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2265G>A",
"hgvs_p": "p.Met755Ile",
"transcript": "XM_047426409.1",
"protein_id": "XP_047282365.1",
"transcript_support_level": null,
"aa_start": 755,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2265,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 2382,
"cdna_end": null,
"cdna_length": 4991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2124G>A",
"hgvs_p": "p.Met708Ile",
"transcript": "XM_047426415.1",
"protein_id": "XP_047282371.1",
"transcript_support_level": null,
"aa_start": 708,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2124,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2241,
"cdna_end": null,
"cdna_length": 4850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.726G>A",
"hgvs_p": "p.Met242Ile",
"transcript": "XM_047426417.1",
"protein_id": "XP_047282373.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 679,
"cds_start": 726,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 3536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.726G>A",
"hgvs_p": "p.Met242Ile",
"transcript": "XM_047426420.1",
"protein_id": "XP_047282376.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 679,
"cds_start": 726,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 3427,
"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": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.1660G>A",
"hgvs_p": null,
"transcript": "ENST00000491302.2",
"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": 3951,
"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": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.6437G>A",
"hgvs_p": null,
"transcript": "ENST00000697630.1",
"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": 7205,
"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": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.*828G>A",
"hgvs_p": null,
"transcript": "ENST00000697633.1",
"protein_id": "ENSP00000513365.1",
"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": 3630,
"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": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.*828G>A",
"hgvs_p": null,
"transcript": "ENST00000697633.1",
"protein_id": "ENSP00000513365.1",
"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": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MIR181A1HG",
"gene_hgnc_id": 48659,
"hgvs_c": "n.422-257C>T",
"hgvs_p": null,
"transcript": "ENST00000806890.1",
"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": 679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"dbsnp": "rs770932386",
"frequency_reference_population": 0.000045899786,
"hom_count_reference_population": 0,
"allele_count_reference_population": 74,
"gnomad_exomes_af": 0.0000486147,
"gnomad_genomes_af": 0.0000197701,
"gnomad_exomes_ac": 71,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8152124881744385,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.547,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9786,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.894,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000442510.8",
"gene_symbol": "PTPRC",
"hgnc_id": 9666,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2607G>A",
"hgvs_p": "p.Met869Ile"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000806890.1",
"gene_symbol": "MIR181A1HG",
"hgnc_id": 48659,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.422-257C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Immunodeficiency 104,Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Immunodeficiency 104|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}