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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: 5-70942430-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=70942430&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 70942430,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000380707.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "NM_000344.4",
"protein_id": "NP_000335.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 294,
"cds_start": 346,
"cds_end": null,
"cds_length": 885,
"cdna_start": 363,
"cdna_end": null,
"cdna_length": 1482,
"mane_select": "ENST00000380707.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "ENST00000380707.9",
"protein_id": "ENSP00000370083.4",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 294,
"cds_start": 346,
"cds_end": null,
"cds_length": 885,
"cdna_start": 363,
"cdna_end": null,
"cdna_length": 1482,
"mane_select": "NM_000344.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "ENST00000351205.8",
"protein_id": "ENSP00000305857.5",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 294,
"cds_start": 346,
"cds_end": null,
"cds_length": 885,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "ENST00000506163.5",
"protein_id": "ENSP00000424926.1",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 282,
"cds_start": 346,
"cds_end": null,
"cds_length": 849,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 1445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "ENST00000625245.2",
"protein_id": "ENSP00000486539.1",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 294,
"cds_start": 346,
"cds_end": null,
"cds_length": 885,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "NM_001297715.1",
"protein_id": "NP_001284644.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 282,
"cds_start": 346,
"cds_end": null,
"cds_length": 849,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "NM_022874.2",
"protein_id": "NP_075012.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 262,
"cds_start": 346,
"cds_end": null,
"cds_length": 789,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "ENST00000503079.6",
"protein_id": "ENSP00000428128.1",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 262,
"cds_start": 346,
"cds_end": null,
"cds_length": 789,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "XM_047417615.1",
"protein_id": "XP_047273571.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 295,
"cds_start": 346,
"cds_end": null,
"cds_length": 888,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "XM_011543596.2",
"protein_id": "XP_011541898.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 294,
"cds_start": 346,
"cds_end": null,
"cds_length": 885,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "XM_047417616.1",
"protein_id": "XP_047273572.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 262,
"cds_start": 346,
"cds_end": null,
"cds_length": 789,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe",
"transcript": "XM_017009786.2",
"protein_id": "XP_016865275.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 250,
"cds_start": 346,
"cds_end": null,
"cds_length": 753,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1478,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "n.346A>T",
"hgvs_p": null,
"transcript": "ENST00000506239.6",
"protein_id": "ENSP00000422679.2",
"transcript_support_level": 5,
"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": 1550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.274-288A>T",
"hgvs_p": null,
"transcript": "ENST00000514951.5",
"protein_id": "ENSP00000423298.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.274-288A>T",
"hgvs_p": null,
"transcript": "XM_011543597.2",
"protein_id": "XP_011541899.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.274-288A>T",
"hgvs_p": null,
"transcript": "XM_047417618.1",
"protein_id": "XP_047273574.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": -4,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "n.-78A>T",
"hgvs_p": null,
"transcript": "ENST00000507905.6",
"protein_id": "ENSP00000430657.1",
"transcript_support_level": 5,
"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": 431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "n.-88A>T",
"hgvs_p": null,
"transcript": "ENST00000513228.1",
"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": 499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "n.-42A>T",
"hgvs_p": null,
"transcript": "ENST00000518504.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"dbsnp": "rs104893933",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8225828409194946,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.23000000417232513,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.521,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2896,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": -0.749,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.23,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000380707.9",
"gene_symbol": "SMN1",
"hgnc_id": 11117,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.346A>T",
"hgvs_p": "p.Ile116Phe"
}
],
"clinvar_disease": "Werdnig-Hoffmann disease,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Werdnig-Hoffmann disease|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}