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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: 19-45488889-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45488889&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45488889,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000245923.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"transcript": "NM_005619.5",
"protein_id": "NP_005610.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 545,
"cds_start": 1339,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1561,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": "ENST00000245923.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"transcript": "ENST00000245923.9",
"protein_id": "ENSP00000245923.3",
"transcript_support_level": 1,
"aa_start": 447,
"aa_end": null,
"aa_length": 545,
"cds_start": 1339,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1561,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": "NM_005619.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374Trp",
"transcript": "ENST00000344680.8",
"protein_id": "ENSP00000345127.3",
"transcript_support_level": 1,
"aa_start": 374,
"aa_end": null,
"aa_length": 472,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1350,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.319C>T",
"hgvs_p": "p.Arg107Trp",
"transcript": "ENST00000430715.6",
"protein_id": "ENSP00000398178.1",
"transcript_support_level": 1,
"aa_start": 107,
"aa_end": null,
"aa_length": 205,
"cds_start": 319,
"cds_end": null,
"cds_length": 618,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 1127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.*337C>T",
"hgvs_p": null,
"transcript": "ENST00000591286.5",
"protein_id": "ENSP00000467863.1",
"transcript_support_level": 1,
"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": 2111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.*337C>T",
"hgvs_p": null,
"transcript": "ENST00000591286.5",
"protein_id": "ENSP00000467863.1",
"transcript_support_level": 1,
"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": 2111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374Trp",
"transcript": "NM_206900.3",
"protein_id": "NP_996783.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 472,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1342,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Arg173Trp",
"transcript": "ENST00000590526.5",
"protein_id": "ENSP00000466619.1",
"transcript_support_level": 5,
"aa_start": 173,
"aa_end": null,
"aa_length": 271,
"cds_start": 517,
"cds_end": null,
"cds_length": 816,
"cdna_start": 1644,
"cdna_end": null,
"cdna_length": 2357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.319C>T",
"hgvs_p": "p.Arg107Trp",
"transcript": "NM_206901.3",
"protein_id": "NP_996784.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 205,
"cds_start": 319,
"cds_end": null,
"cds_length": 618,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 1113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.1339C>T",
"hgvs_p": null,
"transcript": "ENST00000587597.5",
"protein_id": "ENSP00000468144.1",
"transcript_support_level": 5,
"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": 2212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.177C>T",
"hgvs_p": null,
"transcript": "ENST00000588036.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.306C>T",
"hgvs_p": null,
"transcript": "ENST00000589628.1",
"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": 435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.85C>T",
"hgvs_p": null,
"transcript": "ENST00000591789.1",
"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": 682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.215C>T",
"hgvs_p": null,
"transcript": "ENST00000593129.1",
"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": 526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1N",
"gene_hgnc_id": 26845,
"hgvs_c": "c.-106G>A",
"hgvs_p": null,
"transcript": "ENST00000401705.5",
"protein_id": "ENSP00000384318.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": -4,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.62-2776C>T",
"hgvs_p": null,
"transcript": "ENST00000590746.5",
"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": 228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"dbsnp": "rs764827191",
"frequency_reference_population": 0.000012456604,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000130733,
"gnomad_genomes_af": 0.00000656883,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5702214241027832,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.396,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4038,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.69,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000245923.9",
"gene_symbol": "RTN2",
"hgnc_id": 10468,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000401705.5",
"gene_symbol": "PPM1N",
"hgnc_id": 26845,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-106G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary spastic paraplegia 12",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary spastic paraplegia 12",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}