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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: 19-49293994-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49293994&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49293994,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_014037.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "NM_014037.3",
"protein_id": "NP_054756.2",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 736,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000335875.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014037.3"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "ENST00000335875.9",
"protein_id": "ENSP00000338627.3",
"transcript_support_level": 5,
"aa_start": 484,
"aa_end": null,
"aa_length": 736,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014037.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335875.9"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "ENST00000454748.7",
"protein_id": "ENSP00000404022.2",
"transcript_support_level": 1,
"aa_start": 484,
"aa_end": null,
"aa_length": 659,
"cds_start": 1451,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454748.7"
},
{
"aa_ref": "F",
"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": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.86T>C",
"hgvs_p": "p.Phe29Ser",
"transcript": "ENST00000598828.1",
"protein_id": "ENSP00000469885.1",
"transcript_support_level": 2,
"aa_start": 29,
"aa_end": null,
"aa_length": 162,
"cds_start": 86,
"cds_end": null,
"cds_length": 490,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000598828.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1628T>C",
"hgvs_p": "p.Phe543Ser",
"transcript": "XM_047438701.1",
"protein_id": "XP_047294657.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 795,
"cds_start": 1628,
"cds_end": null,
"cds_length": 2388,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438701.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1628T>C",
"hgvs_p": "p.Phe543Ser",
"transcript": "XM_047438702.1",
"protein_id": "XP_047294658.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 795,
"cds_start": 1628,
"cds_end": null,
"cds_length": 2388,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438702.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1520T>C",
"hgvs_p": "p.Phe507Ser",
"transcript": "XM_047438703.1",
"protein_id": "XP_047294659.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 759,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438703.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1517T>C",
"hgvs_p": "p.Phe506Ser",
"transcript": "XM_011526860.3",
"protein_id": "XP_011525162.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 758,
"cds_start": 1517,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526860.3"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "XM_005258820.4",
"protein_id": "XP_005258877.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 736,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005258820.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "XM_006723168.4",
"protein_id": "XP_006723231.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 736,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723168.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser",
"transcript": "XM_024451472.2",
"protein_id": "XP_024307240.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 736,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451472.2"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1340T>C",
"hgvs_p": "p.Phe447Ser",
"transcript": "XM_011526859.4",
"protein_id": "XP_011525161.3",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 699,
"cds_start": 1340,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526859.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1010T>C",
"hgvs_p": "p.Phe337Ser",
"transcript": "XM_011526861.4",
"protein_id": "XP_011525163.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 589,
"cds_start": 1010,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526861.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "c.1010T>C",
"hgvs_p": "p.Phe337Ser",
"transcript": "XM_047438704.1",
"protein_id": "XP_047294660.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 589,
"cds_start": 1010,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438704.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"hgvs_c": "n.307T>C",
"hgvs_p": null,
"transcript": "ENST00000598221.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000598221.1"
}
],
"gene_symbol": "SLC6A16",
"gene_hgnc_id": 13622,
"dbsnp": "rs757241071",
"frequency_reference_population": 0.000022317443,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000239574,
"gnomad_genomes_af": 0.00000657203,
"gnomad_exomes_ac": 35,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9135034084320068,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.547,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.436,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.548,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014037.3",
"gene_symbol": "SLC6A16",
"hgnc_id": 13622,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Phe484Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}