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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: 3-38722404-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38722404&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38722404,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006514.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3361C>A",
"hgvs_p": "p.Arg1121Ser",
"transcript": "NM_006514.4",
"protein_id": "NP_006505.4",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1956,
"cds_start": 3361,
"cds_end": null,
"cds_length": 5871,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000449082.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006514.4"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3361C>A",
"hgvs_p": "p.Arg1121Ser",
"transcript": "ENST00000449082.3",
"protein_id": "ENSP00000390600.2",
"transcript_support_level": 1,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1956,
"cds_start": 3361,
"cds_end": null,
"cds_length": 5871,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006514.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449082.3"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3358C>A",
"hgvs_p": "p.Arg1120Ser",
"transcript": "ENST00000643924.1",
"protein_id": "ENSP00000495595.1",
"transcript_support_level": null,
"aa_start": 1120,
"aa_end": null,
"aa_length": 1955,
"cds_start": 3358,
"cds_end": null,
"cds_length": 5868,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000643924.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3385C>A",
"hgvs_p": "p.Arg1129Ser",
"transcript": "ENST00000655275.1",
"protein_id": "ENSP00000499510.1",
"transcript_support_level": null,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1964,
"cds_start": 3385,
"cds_end": null,
"cds_length": 5895,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000655275.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3358C>A",
"hgvs_p": "p.Arg1120Ser",
"transcript": "NM_001293306.2",
"protein_id": "NP_001280235.2",
"transcript_support_level": null,
"aa_start": 1120,
"aa_end": null,
"aa_length": 1955,
"cds_start": 3358,
"cds_end": null,
"cds_length": 5868,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001293306.2"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3067C>A",
"hgvs_p": "p.Arg1023Ser",
"transcript": "NM_001293307.2",
"protein_id": "NP_001280236.2",
"transcript_support_level": null,
"aa_start": 1023,
"aa_end": null,
"aa_length": 1858,
"cds_start": 3067,
"cds_end": null,
"cds_length": 5577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001293307.2"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3370C>A",
"hgvs_p": "p.Arg1124Ser",
"transcript": "XM_005265371.4",
"protein_id": "XP_005265428.1",
"transcript_support_level": null,
"aa_start": 1124,
"aa_end": null,
"aa_length": 1959,
"cds_start": 3370,
"cds_end": null,
"cds_length": 5880,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265371.4"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3367C>A",
"hgvs_p": "p.Arg1123Ser",
"transcript": "XM_011533993.3",
"protein_id": "XP_011532295.1",
"transcript_support_level": null,
"aa_start": 1123,
"aa_end": null,
"aa_length": 1958,
"cds_start": 3367,
"cds_end": null,
"cds_length": 5877,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533993.3"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3076C>A",
"hgvs_p": "p.Arg1026Ser",
"transcript": "XM_011533994.3",
"protein_id": "XP_011532296.1",
"transcript_support_level": null,
"aa_start": 1026,
"aa_end": null,
"aa_length": 1861,
"cds_start": 3076,
"cds_end": null,
"cds_length": 5586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533994.3"
}
],
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"dbsnp": "rs146965005",
"frequency_reference_population": 0.000079330355,
"hom_count_reference_population": 0,
"allele_count_reference_population": 128,
"gnomad_exomes_af": 0.0000417461,
"gnomad_genomes_af": 0.00043995,
"gnomad_exomes_ac": 61,
"gnomad_genomes_ac": 67,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.032620906829833984,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.335,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1864,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.386,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006514.4",
"gene_symbol": "SCN10A",
"hgnc_id": 10582,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.3361C>A",
"hgvs_p": "p.Arg1121Ser"
}
],
"clinvar_disease": "Brugada syndrome,Cardiovascular phenotype,SCN10A-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Brugada syndrome|not provided|Cardiovascular phenotype|SCN10A-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}