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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: 6-42925297-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42925297&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PTCRA",
"hgnc_id": 21290,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001243168.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 22,
"alphamissense_prediction": null,
"alphamissense_score": 0.3722,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "6",
"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": 0.5689010620117188,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 281,
"aa_ref": "R",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1019,
"cdna_start": 478,
"cds_end": null,
"cds_length": 846,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_138296.3",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.461G>A",
"hgvs_p": "p.Arg154Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000304672.6",
"protein_coding": true,
"protein_id": "NP_612153.2",
"strand": true,
"transcript": "NM_138296.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 281,
"aa_ref": "R",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1019,
"cdna_start": 478,
"cds_end": null,
"cds_length": 846,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000304672.6",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.461G>A",
"hgvs_p": "p.Arg154Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138296.3",
"protein_coding": true,
"protein_id": "ENSP00000304447.2",
"strand": true,
"transcript": "ENST00000304672.6",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 256,
"aa_ref": "R",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1005,
"cdna_start": 467,
"cds_end": null,
"cds_length": 771,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000441198.4",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.386G>A",
"hgvs_p": "p.Arg129Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000409550.1",
"strand": true,
"transcript": "ENST00000441198.4",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 174,
"aa_ref": "R",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 759,
"cdna_start": 221,
"cds_end": null,
"cds_length": 525,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000446507.5",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.140G>A",
"hgvs_p": "p.Arg47Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392288.1",
"strand": true,
"transcript": "ENST00000446507.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1064,
"cdna_start": 523,
"cds_end": null,
"cds_length": 891,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001243168.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230097.1",
"strand": true,
"transcript": "NM_001243168.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1125,
"cdna_start": 587,
"cds_end": null,
"cds_length": 891,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000616441.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477815.1",
"strand": true,
"transcript": "ENST00000616441.2",
"transcript_support_level": 2
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 256,
"aa_ref": "R",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 944,
"cdna_start": 403,
"cds_end": null,
"cds_length": 771,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001243169.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.386G>A",
"hgvs_p": "p.Arg129Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230098.1",
"strand": true,
"transcript": "NM_001243169.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 174,
"aa_ref": "R",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 698,
"cdna_start": 157,
"cds_end": null,
"cds_length": 525,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001243170.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.140G>A",
"hgvs_p": "p.Arg47Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230099.1",
"strand": true,
"transcript": "NM_001243170.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 248,
"aa_ref": "R",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1051,
"cdna_start": 510,
"cds_end": null,
"cds_length": 747,
"cds_start": 362,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_024446342.1",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.362G>A",
"hgvs_p": "p.Arg121Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024302110.1",
"strand": true,
"transcript": "XM_024446342.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 203,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 977,
"cdna_start": null,
"cds_end": null,
"cds_length": 612,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024446344.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.457-49G>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024302112.1",
"strand": true,
"transcript": "XM_024446344.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 187,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 966,
"cdna_start": null,
"cds_end": null,
"cds_length": 564,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024446345.1",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.409-49G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024302113.1",
"strand": true,
"transcript": "XM_024446345.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 153,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 816,
"cdna_start": null,
"cds_end": null,
"cds_length": 462,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024446346.2",
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"hgvs_c": "c.307-49G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024302114.1",
"strand": true,
"transcript": "XM_024446346.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs745333497",
"effect": "missense_variant",
"frequency_reference_population": 0.000013845464,
"gene_hgnc_id": 21290,
"gene_symbol": "PTCRA",
"gnomad_exomes_ac": 21,
"gnomad_exomes_af": 0.0000146153,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657376,
"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": "Benign",
"phylop100way_score": 3.377,
"pos": 42925297,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.242,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10999999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.11,
"transcript": "NM_001243168.2"
}
]
}