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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: 5-150521294-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=150521294&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 150521294,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001543.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "NM_001543.5",
"protein_id": "NP_001534.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 882,
"cds_start": 40,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 8011,
"mane_select": "ENST00000261797.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "ENST00000261797.7",
"protein_id": "ENSP00000261797.6",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 882,
"cds_start": 40,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 8011,
"mane_select": "NM_001543.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "NM_001301063.2",
"protein_id": "NP_001287992.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 825,
"cds_start": 40,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 628,
"cdna_end": null,
"cdna_length": 7945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "ENST00000523767.5",
"protein_id": "ENSP00000428604.1",
"transcript_support_level": 2,
"aa_start": 14,
"aa_end": null,
"aa_length": 825,
"cds_start": 40,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 629,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "ENST00000519157.1",
"protein_id": "ENSP00000427813.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 158,
"cds_start": 40,
"cds_end": null,
"cds_length": 477,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "ENST00000522491.1",
"protein_id": "ENSP00000429966.1",
"transcript_support_level": 2,
"aa_start": 14,
"aa_end": null,
"aa_length": 67,
"cds_start": 40,
"cds_end": null,
"cds_length": 204,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met",
"transcript": "ENST00000518299.1",
"protein_id": "ENSP00000430258.1",
"transcript_support_level": 2,
"aa_start": 14,
"aa_end": null,
"aa_length": 22,
"cds_start": 40,
"cds_end": null,
"cds_length": 69,
"cdna_start": 740,
"cdna_end": null,
"cdna_length": 769,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "n.*192G>A",
"hgvs_p": null,
"transcript": "ENST00000518346.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 496,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"hgvs_c": "n.*67G>A",
"hgvs_p": null,
"transcript": "ENST00000524161.1",
"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": 437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NDST1",
"gene_hgnc_id": 7680,
"dbsnp": "rs377262041",
"frequency_reference_population": 0.00003287095,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000315044,
"gnomad_genomes_af": 0.0000459758,
"gnomad_exomes_ac": 46,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07440787553787231,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.055,
"revel_prediction": "Benign",
"alphamissense_score": 0.1186,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.443,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_001543.5",
"gene_symbol": "NDST1",
"hgnc_id": 7680,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Met"
}
],
"clinvar_disease": "Intellectual disability",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Intellectual disability",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}