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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: 4-56966658-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56966658&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NOA1",
"hgnc_id": 28473,
"hgvs_c": "c.1726G>A",
"hgvs_p": "p.Ala576Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_032313.4",
"verdict": "Likely_benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "REST",
"hgnc_id": 9966,
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Arg329Cys",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -10,
"transcript": "ENST00000640343.2",
"verdict": "Benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_score": -4,
"allele_count_reference_population": 33,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0712,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.81,
"chr": "4",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.058804869651794434,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 698,
"aa_ref": "A",
"aa_start": 576,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2218,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 2097,
"cds_start": 1726,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_032313.4",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1726G>A",
"hgvs_p": "p.Ala576Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264230.5",
"protein_coding": true,
"protein_id": "NP_115689.1",
"strand": false,
"transcript": "NM_032313.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 698,
"aa_ref": "A",
"aa_start": 576,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2218,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 2097,
"cds_start": 1726,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000264230.5",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1726G>A",
"hgvs_p": "p.Ala576Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032313.4",
"protein_coding": true,
"protein_id": "ENSP00000264230.4",
"strand": false,
"transcript": "ENST00000264230.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 335,
"aa_ref": "R",
"aa_start": 329,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1264,
"cdna_start": 1114,
"cds_end": null,
"cds_length": 1008,
"cds_start": 985,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000640343.2",
"gene_hgnc_id": 9966,
"gene_symbol": "REST",
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Arg329Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492813.1",
"strand": true,
"transcript": "ENST00000640343.2",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 307,
"aa_ref": "R",
"aa_start": 301,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1328,
"cdna_start": 1248,
"cds_end": null,
"cds_length": 924,
"cds_start": 901,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000640168.2",
"gene_hgnc_id": 9966,
"gene_symbol": "REST",
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Arg301Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490969.1",
"strand": true,
"transcript": "ENST00000640168.2",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 706,
"aa_ref": "A",
"aa_start": 584,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2231,
"cdna_start": 1758,
"cds_end": null,
"cds_length": 2121,
"cds_start": 1750,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000904433.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Ala584Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574492.1",
"strand": false,
"transcript": "ENST00000904433.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 695,
"aa_ref": "A",
"aa_start": 573,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2211,
"cdna_start": 1737,
"cds_end": null,
"cds_length": 2088,
"cds_start": 1717,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000904430.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1717G>A",
"hgvs_p": "p.Ala573Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574489.1",
"strand": false,
"transcript": "ENST00000904430.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 681,
"aa_ref": "A",
"aa_start": 559,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2164,
"cdna_start": 1695,
"cds_end": null,
"cds_length": 2046,
"cds_start": 1675,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000904431.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1675G>A",
"hgvs_p": "p.Ala559Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574490.1",
"strand": false,
"transcript": "ENST00000904431.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 654,
"aa_ref": "A",
"aa_start": 532,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2559,
"cdna_start": 1614,
"cds_end": null,
"cds_length": 1965,
"cds_start": 1594,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000933297.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1594G>A",
"hgvs_p": "p.Ala532Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603356.1",
"strand": false,
"transcript": "ENST00000933297.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 659,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2590,
"cdna_start": null,
"cds_end": null,
"cds_length": 1980,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000904429.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1647+1726G>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574488.1",
"strand": false,
"transcript": "ENST00000904429.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 615,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1965,
"cdna_start": null,
"cds_end": null,
"cds_length": 1848,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000904432.1",
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"hgvs_c": "c.1516-2132G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574491.1",
"strand": false,
"transcript": "ENST00000904432.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs781753631",
"effect": "missense_variant",
"frequency_reference_population": 0.000020452584,
"gene_hgnc_id": 28473,
"gene_symbol": "NOA1",
"gnomad_exomes_ac": 30,
"gnomad_exomes_af": 0.000020529,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197184,
"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": "Likely benign",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.095,
"pos": 56966658,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.033,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_032313.4"
}
]
}