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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: 16-4783690-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=4783690&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 4783690,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000268231.13",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.589G>A",
"hgvs_p": "p.Asp197Asn",
"transcript": "NM_144605.5",
"protein_id": "NP_653206.2",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 358,
"cds_start": 589,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 1356,
"mane_select": "ENST00000268231.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.589G>A",
"hgvs_p": "p.Asp197Asn",
"transcript": "ENST00000268231.13",
"protein_id": "ENSP00000268231.8",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 358,
"cds_start": 589,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 1356,
"mane_select": "NM_144605.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Asp151Asn",
"transcript": "ENST00000396693.9",
"protein_id": "ENSP00000379922.4",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 312,
"cds_start": 451,
"cds_end": null,
"cds_length": 939,
"cdna_start": 540,
"cdna_end": null,
"cdna_length": 1156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Asp151Asn",
"transcript": "NM_001154458.3",
"protein_id": "NP_001147930.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 312,
"cds_start": 451,
"cds_end": null,
"cds_length": 939,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 1218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Asp203Asn",
"transcript": "XM_017022938.2",
"protein_id": "XP_016878427.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 364,
"cds_start": 607,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1185,
"cdna_end": null,
"cdna_length": 1864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.589G>A",
"hgvs_p": "p.Asp197Asn",
"transcript": "XM_006720846.3",
"protein_id": "XP_006720909.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 358,
"cds_start": 589,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1040,
"cdna_end": null,
"cdna_length": 1719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.589G>A",
"hgvs_p": "p.Asp197Asn",
"transcript": "XM_024450155.2",
"protein_id": "XP_024305923.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 358,
"cds_start": 589,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1036,
"cdna_end": null,
"cdna_length": 1715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Asp133Asn",
"transcript": "XM_011522379.4",
"protein_id": "XP_011520681.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 294,
"cds_start": 397,
"cds_end": null,
"cds_length": 885,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 1263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "n.589G>A",
"hgvs_p": null,
"transcript": "ENST00000587603.5",
"protein_id": "ENSP00000467237.1",
"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": 1436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "n.29+2117G>A",
"hgvs_p": null,
"transcript": "ENST00000588241.5",
"protein_id": "ENSP00000464775.1",
"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": 509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285952",
"gene_hgnc_id": null,
"hgvs_c": "n.2025+2117G>A",
"hgvs_p": null,
"transcript": "ENST00000649556.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"hgvs_c": "n.*590G>A",
"hgvs_p": null,
"transcript": "ENST00000590741.5",
"protein_id": "ENSP00000468601.1",
"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": 618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEPTIN12",
"gene_hgnc_id": 26348,
"dbsnp": "rs371195126",
"frequency_reference_population": 0.000014250521,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000143664,
"gnomad_genomes_af": 0.000013138,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9644275903701782,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.82,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8773,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.806,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"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": "Uncertain_significance",
"acmg_criteria": "PP3_Strong",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000268231.13",
"gene_symbol": "SEPTIN12",
"hgnc_id": 26348,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.589G>A",
"hgvs_p": "p.Asp197Asn"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000649556.1",
"gene_symbol": "ENSG00000285952",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2025+2117G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Spermatogenic failure 10",
"clinvar_classification": "risk factor",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Spermatogenic failure 10",
"pathogenicity_classification_combined": "risk factor",
"custom_annotations": null
}
],
"message": null
}