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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: 1-9982577-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=9982577&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 9982577,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000377205.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser",
"transcript": "NM_022787.4",
"protein_id": "NP_073624.2",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 279,
"cds_start": 716,
"cds_end": null,
"cds_length": 840,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": "ENST00000377205.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser",
"transcript": "ENST00000377205.6",
"protein_id": "ENSP00000366410.1",
"transcript_support_level": 1,
"aa_start": 239,
"aa_end": null,
"aa_length": 279,
"cds_start": 716,
"cds_end": null,
"cds_length": 840,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": "NM_022787.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser",
"transcript": "NM_001297778.1",
"protein_id": "NP_001284707.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 279,
"cds_start": 716,
"cds_end": null,
"cds_length": 840,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 3796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser",
"transcript": "XM_017002107.3",
"protein_id": "XP_016857596.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 279,
"cds_start": 716,
"cds_end": null,
"cds_length": 840,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 3990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser",
"transcript": "XM_047428076.1",
"protein_id": "XP_047284032.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 279,
"cds_start": 716,
"cds_end": null,
"cds_length": 840,
"cdna_start": 2267,
"cdna_end": null,
"cdna_length": 5188,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "n.716T>C",
"hgvs_p": null,
"transcript": "ENST00000462686.1",
"protein_id": "ENSP00000435134.1",
"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": 1818,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.118+1407T>C",
"hgvs_p": null,
"transcript": "ENST00000496751.1",
"protein_id": "ENSP00000467340.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 41,
"cds_start": -4,
"cds_end": null,
"cds_length": 126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 485,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.439+1407T>C",
"hgvs_p": null,
"transcript": "XM_017002108.3",
"protein_id": "XP_016857597.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 150,
"cds_start": -4,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 718,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"hgvs_c": "c.439+1407T>C",
"hgvs_p": null,
"transcript": "XM_011541971.2",
"protein_id": "XP_011540273.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NMNAT1",
"gene_hgnc_id": 17877,
"dbsnp": "rs778606847",
"frequency_reference_population": 0.0000049565742,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000342023,
"gnomad_genomes_af": 0.00001972,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9648771286010742,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.977,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8722,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.433,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000377205.6",
"gene_symbol": "NMNAT1",
"hgnc_id": 17877,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.716T>C",
"hgvs_p": "p.Leu239Ser"
}
],
"clinvar_disease": "Leber congenital amaurosis 9,Retinal dystrophy",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Leber congenital amaurosis 9|Retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}