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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: 4-158713151-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=158713151&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 158713151,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005038.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Asn288Asp",
"transcript": "NM_005038.3",
"protein_id": "NP_005029.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 370,
"cds_start": 862,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 970,
"cdna_end": null,
"cdna_length": 1830,
"mane_select": "ENST00000307720.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005038.3"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Asn288Asp",
"transcript": "ENST00000307720.4",
"protein_id": "ENSP00000303754.3",
"transcript_support_level": 1,
"aa_start": 288,
"aa_end": null,
"aa_length": 370,
"cds_start": 862,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 970,
"cdna_end": null,
"cdna_length": 1830,
"mane_select": "NM_005038.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307720.4"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.844A>G",
"hgvs_p": "p.Asn282Asp",
"transcript": "ENST00000877683.1",
"protein_id": "ENSP00000547742.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 364,
"cds_start": 844,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 929,
"cdna_end": null,
"cdna_length": 1782,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877683.1"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.829A>G",
"hgvs_p": "p.Asn277Asp",
"transcript": "ENST00000877682.1",
"protein_id": "ENSP00000547741.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 359,
"cds_start": 829,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 940,
"cdna_end": null,
"cdna_length": 1790,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877682.1"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.802A>G",
"hgvs_p": "p.Asn268Asp",
"transcript": "ENST00000914202.1",
"protein_id": "ENSP00000584261.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 350,
"cds_start": 802,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 1753,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914202.1"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.739A>G",
"hgvs_p": "p.Asn247Asp",
"transcript": "ENST00000914201.1",
"protein_id": "ENSP00000584260.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 329,
"cds_start": 739,
"cds_end": null,
"cds_length": 990,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 1710,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914201.1"
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.673A>G",
"hgvs_p": "p.Asn225Asp",
"transcript": "ENST00000914203.1",
"protein_id": "ENSP00000584262.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 307,
"cds_start": 673,
"cds_end": null,
"cds_length": 924,
"cdna_start": 748,
"cdna_end": null,
"cdna_length": 1606,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914203.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.523-2303A>G",
"hgvs_p": null,
"transcript": "ENST00000953196.1",
"protein_id": "ENSP00000623255.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": null,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1427,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953196.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "n.*309A>G",
"hgvs_p": null,
"transcript": "ENST00000512699.1",
"protein_id": "ENSP00000423207.1",
"transcript_support_level": 3,
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512699.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "n.*309A>G",
"hgvs_p": null,
"transcript": "ENST00000512699.1",
"protein_id": "ENSP00000423207.1",
"transcript_support_level": 3,
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512699.1"
}
],
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"dbsnp": "rs751192669",
"frequency_reference_population": 0.000003097928,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000205235,
"gnomad_genomes_af": 0.0000131372,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.036759018898010254,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.114,
"revel_prediction": "Benign",
"alphamissense_score": 0.0495,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.379,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_005038.3",
"gene_symbol": "PPID",
"hgnc_id": 9257,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Asn288Asp"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}