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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: 14-74484420-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=74484420&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 74484420,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001363688.1",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "NM_006432.5",
"protein_id": "NP_006423.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 151,
"cds_start": 358,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000555619.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006432.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000555619.6",
"protein_id": "ENSP00000451112.2",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 151,
"cds_start": 358,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006432.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555619.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000557510.5",
"protein_id": "ENSP00000451206.1",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 174,
"cds_start": 358,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000557510.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000553490.5",
"protein_id": "ENSP00000451180.1",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 220,
"cds_start": 358,
"cds_end": null,
"cds_length": 664,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000553490.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000434013.6",
"protein_id": "ENSP00000412103.2",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 201,
"cds_start": 358,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434013.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "NM_001363688.1",
"protein_id": "NP_001350617.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 174,
"cds_start": 358,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363688.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.421C>T",
"hgvs_p": "p.Pro141Ser",
"transcript": "ENST00000556009.5",
"protein_id": "ENSP00000450502.1",
"transcript_support_level": 5,
"aa_start": 141,
"aa_end": null,
"aa_length": 172,
"cds_start": 421,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556009.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.415C>T",
"hgvs_p": "p.Pro139Ser",
"transcript": "ENST00000932868.1",
"protein_id": "ENSP00000602926.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 170,
"cds_start": 415,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932868.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000238633.6",
"protein_id": "ENSP00000238633.2",
"transcript_support_level": 3,
"aa_start": 120,
"aa_end": null,
"aa_length": 148,
"cds_start": 358,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000238633.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "NM_001375440.1",
"protein_id": "NP_001362369.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 125,
"cds_start": 358,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001375440.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000541064.5",
"protein_id": "ENSP00000442488.1",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 125,
"cds_start": 358,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541064.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser",
"transcript": "ENST00000555592.1",
"protein_id": "ENSP00000450887.1",
"transcript_support_level": 5,
"aa_start": 120,
"aa_end": null,
"aa_length": 121,
"cds_start": 358,
"cds_end": null,
"cds_length": 367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555592.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Pro84Ser",
"transcript": "ENST00000851979.1",
"protein_id": "ENSP00000522038.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 115,
"cds_start": 250,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851979.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.114+1985C>T",
"hgvs_p": null,
"transcript": "ENST00000932865.1",
"protein_id": "ENSP00000602925.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 68,
"cds_start": null,
"cds_end": null,
"cds_length": 207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932865.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "n.158+1909C>T",
"hgvs_p": null,
"transcript": "ENST00000554482.1",
"protein_id": "ENSP00000451314.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000554482.1"
}
],
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"dbsnp": "rs104894458",
"frequency_reference_population": 0.000002052194,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205219,
"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": 0.9925535917282104,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.921,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9527,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.754,
"phylop100way_prediction": "Pathogenic",
"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": 20,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 20,
"benign_score": 0,
"pathogenic_score": 20,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001363688.1",
"gene_symbol": "NPC2",
"hgnc_id": 14537,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.358C>T",
"hgvs_p": "p.Pro120Ser"
}
],
"clinvar_disease": " type C, type C1, type C2,Niemann-Pick disease",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Niemann-Pick disease, type C2|Niemann-Pick disease, type C1|Niemann-Pick disease, type C",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}