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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: 4-56490591-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56490591&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SRP72",
"hgnc_id": 11303,
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_006947.4",
"verdict": "Likely_benign"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000289393",
"hgnc_id": 58796,
"hgvs_c": "n.133-12820G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000737350.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 83,
"alphamissense_prediction": null,
"alphamissense_score": 0.4318,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.14,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7180453538894653,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 671,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3855,
"cdna_start": 1467,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1448,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_006947.4",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000642900.1",
"protein_coding": true,
"protein_id": "NP_008878.3",
"strand": true,
"transcript": "NM_006947.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 671,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3855,
"cdna_start": 1467,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1448,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000642900.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006947.4",
"protein_coding": true,
"protein_id": "ENSP00000495128.1",
"strand": true,
"transcript": "ENST00000642900.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 610,
"aa_ref": "T",
"aa_start": 422,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2406,
"cdna_start": 1284,
"cds_end": null,
"cds_length": 1833,
"cds_start": 1265,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000510663.6",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1265C>A",
"hgvs_p": "p.Thr422Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424576.1",
"strand": true,
"transcript": "ENST00000510663.6",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 669,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3300,
"cdna_start": 1489,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1448,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000925431.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595490.1",
"strand": true,
"transcript": "ENST00000925431.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 610,
"aa_ref": "T",
"aa_start": 422,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3672,
"cdna_start": 1284,
"cds_end": null,
"cds_length": 1833,
"cds_start": 1265,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001267722.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1265C>A",
"hgvs_p": "p.Thr422Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254651.1",
"strand": true,
"transcript": "NM_001267722.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 566,
"aa_ref": "T",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 1701,
"cds_start": 1133,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000925432.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1133C>A",
"hgvs_p": "p.Thr378Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595491.1",
"strand": true,
"transcript": "ENST00000925432.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 548,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3079,
"cdna_start": 1467,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1448,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_024454192.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309960.1",
"strand": true,
"transcript": "XM_024454192.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 766,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000646579.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "n.459C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000646579.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 778,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000647432.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "n.550C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000647432.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3969,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NR_151856.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "n.1467C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_151856.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1060,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000737350.1",
"gene_hgnc_id": 58796,
"gene_symbol": "ENSG00000289393",
"hgvs_c": "n.133-12820G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000737350.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs768437750",
"effect": "missense_variant",
"frequency_reference_population": 0.00005143204,
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"gnomad_exomes_ac": 77,
"gnomad_exomes_af": 0.0000526806,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394374,
"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|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.834,
"pos": 56490591,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.505,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006947.4"
}
]
}