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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: 5-476619-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=476619&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 476619,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004174.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln",
"transcript": "NM_004174.4",
"protein_id": "NP_004165.2",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 834,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264938.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004174.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln",
"transcript": "ENST00000264938.8",
"protein_id": "ENSP00000264938.3",
"transcript_support_level": 1,
"aa_start": 605,
"aa_end": null,
"aa_length": 834,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004174.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264938.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"hgvs_c": "c.1787G>A",
"hgvs_p": "p.Arg596Gln",
"transcript": "ENST00000514375.1",
"protein_id": "ENSP00000422983.1",
"transcript_support_level": 1,
"aa_start": 596,
"aa_end": null,
"aa_length": 825,
"cds_start": 1787,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514375.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln",
"transcript": "ENST00000644203.1",
"protein_id": "ENSP00000495903.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 889,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644203.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"hgvs_c": "c.1787G>A",
"hgvs_p": "p.Arg596Gln",
"transcript": "NM_001284351.3",
"protein_id": "NP_001271280.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 825,
"cds_start": 1787,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284351.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC9A3-AS1",
"gene_hgnc_id": 40550,
"hgvs_c": "n.679+56C>T",
"hgvs_p": null,
"transcript": "ENST00000607286.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "pseudogene",
"feature": "ENST00000607286.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC9A3-AS1",
"gene_hgnc_id": 40550,
"hgvs_c": "n.156+56C>T",
"hgvs_p": null,
"transcript": "ENST00000658225.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000658225.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC9A3-AS1",
"gene_hgnc_id": 40550,
"hgvs_c": "n.29+56C>T",
"hgvs_p": null,
"transcript": "ENST00000667998.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000667998.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC9A3-AS1",
"gene_hgnc_id": 40550,
"hgvs_c": "n.679+56C>T",
"hgvs_p": null,
"transcript": "NR_125375.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_125375.1"
},
{
"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": "SLC9A3-AS1",
"gene_hgnc_id": 40550,
"hgvs_c": "n.*129C>T",
"hgvs_p": null,
"transcript": "ENST00000606319.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000606319.1"
}
],
"gene_symbol": "SLC9A3",
"gene_hgnc_id": 11073,
"dbsnp": "rs146547322",
"frequency_reference_population": 0.000212477,
"hom_count_reference_population": 0,
"allele_count_reference_population": 342,
"gnomad_exomes_af": 0.000214103,
"gnomad_genomes_af": 0.000196925,
"gnomad_exomes_ac": 312,
"gnomad_genomes_ac": 30,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008811086416244507,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.198,
"revel_prediction": "Benign",
"alphamissense_score": 0.116,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.516,
"phylop100way_prediction": "Benign",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_004174.4",
"gene_symbol": "SLC9A3",
"hgnc_id": 11073,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NR_125375.1",
"gene_symbol": "SLC9A3-AS1",
"hgnc_id": 40550,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.679+56C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital secretory sodium diarrhea 8,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Congenital secretory sodium diarrhea 8|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}