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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: 17-822445-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=822445&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 822445,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000336868.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.625C>T",
"hgvs_p": "p.Arg209*",
"transcript": "NM_022463.5",
"protein_id": "NP_071908.2",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 435,
"cds_start": 625,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3045,
"mane_select": "ENST00000336868.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.625C>T",
"hgvs_p": "p.Arg209*",
"transcript": "ENST00000336868.8",
"protein_id": "ENSP00000337443.3",
"transcript_support_level": 1,
"aa_start": 209,
"aa_end": null,
"aa_length": 435,
"cds_start": 625,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3045,
"mane_select": "NM_022463.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.301C>T",
"hgvs_p": "p.Arg101*",
"transcript": "ENST00000575801.5",
"protein_id": "ENSP00000461038.1",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 327,
"cds_start": 301,
"cds_end": null,
"cds_length": 984,
"cdna_start": 362,
"cdna_end": null,
"cdna_length": 2681,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "n.394C>T",
"hgvs_p": null,
"transcript": "ENST00000575455.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.-123C>T",
"hgvs_p": null,
"transcript": "ENST00000537628.6",
"protein_id": "ENSP00000446446.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 186,
"cds_start": -4,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.301C>T",
"hgvs_p": "p.Arg101*",
"transcript": "NM_001205319.1",
"protein_id": "NP_001192248.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 327,
"cds_start": 301,
"cds_end": null,
"cds_length": 984,
"cdna_start": 362,
"cdna_end": null,
"cdna_length": 2681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.187C>T",
"hgvs_p": "p.Arg63*",
"transcript": "ENST00000571684.5",
"protein_id": "ENSP00000461562.1",
"transcript_support_level": 3,
"aa_start": 63,
"aa_end": null,
"aa_length": 229,
"cds_start": 187,
"cds_end": null,
"cds_length": 690,
"cdna_start": 188,
"cdna_end": null,
"cdna_length": 1159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.625C>T",
"hgvs_p": "p.Arg209*",
"transcript": "XM_005256756.5",
"protein_id": "XP_005256813.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 375,
"cds_start": 625,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 2865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Arg96*",
"transcript": "XM_005256758.4",
"protein_id": "XP_005256815.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 322,
"cds_start": 286,
"cds_end": null,
"cds_length": 969,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 3599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.625C>T",
"hgvs_p": "p.Arg209*",
"transcript": "XM_017024949.2",
"protein_id": "XP_016880438.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 321,
"cds_start": 625,
"cds_end": null,
"cds_length": 966,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 2510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.301C>T",
"hgvs_p": "p.Arg101*",
"transcript": "XM_047436532.1",
"protein_id": "XP_047292488.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 267,
"cds_start": 301,
"cds_end": null,
"cds_length": 804,
"cdna_start": 362,
"cdna_end": null,
"cdna_length": 2504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"hgvs_c": "c.-123C>T",
"hgvs_p": null,
"transcript": "ENST00000537628.6",
"protein_id": "ENSP00000446446.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 186,
"cds_start": -4,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NXN",
"gene_hgnc_id": 18008,
"dbsnp": "rs1555610590",
"frequency_reference_population": 0.0000020524947,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205249,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.507,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000336868.8",
"gene_symbol": "NXN",
"hgnc_id": 18008,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.625C>T",
"hgvs_p": "p.Arg209*"
}
],
"clinvar_disease": " autosomal recessive 2,Distal shortening of limbs,Robinow syndrome,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "Distal shortening of limbs|Robinow syndrome, autosomal recessive 2|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}