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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: 19-45488676-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45488676&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45488676,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000245923.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"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": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1411G>T",
"hgvs_p": "p.Val471Leu",
"transcript": "NM_005619.5",
"protein_id": "NP_005610.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 545,
"cds_start": 1411,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": "ENST00000245923.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"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": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.1411G>T",
"hgvs_p": "p.Val471Leu",
"transcript": "ENST00000245923.9",
"protein_id": "ENSP00000245923.3",
"transcript_support_level": 1,
"aa_start": 471,
"aa_end": null,
"aa_length": 545,
"cds_start": 1411,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": "NM_005619.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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": "c.1192G>T",
"hgvs_p": "p.Val398Leu",
"transcript": "ENST00000344680.8",
"protein_id": "ENSP00000345127.3",
"transcript_support_level": 1,
"aa_start": 398,
"aa_end": null,
"aa_length": 472,
"cds_start": 1192,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.391G>T",
"hgvs_p": "p.Val131Leu",
"transcript": "ENST00000430715.6",
"protein_id": "ENSP00000398178.1",
"transcript_support_level": 1,
"aa_start": 131,
"aa_end": null,
"aa_length": 205,
"cds_start": 391,
"cds_end": null,
"cds_length": 618,
"cdna_start": 486,
"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": 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.*409G>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": 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.*409G>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": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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": "c.1192G>T",
"hgvs_p": "p.Val398Leu",
"transcript": "NM_206900.3",
"protein_id": "NP_996783.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 472,
"cds_start": 1192,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1414,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.589G>T",
"hgvs_p": "p.Val197Leu",
"transcript": "ENST00000590526.5",
"protein_id": "ENSP00000466619.1",
"transcript_support_level": 5,
"aa_start": 197,
"aa_end": null,
"aa_length": 271,
"cds_start": 589,
"cds_end": null,
"cds_length": 816,
"cdna_start": 1716,
"cdna_end": null,
"cdna_length": 2357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.391G>T",
"hgvs_p": "p.Val131Leu",
"transcript": "NM_206901.3",
"protein_id": "NP_996784.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 205,
"cds_start": 391,
"cds_end": null,
"cds_length": 618,
"cdna_start": 472,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.249G>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": 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.298G>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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.287G>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": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.1381-159G>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": [
"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.62-2563G>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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1N",
"gene_hgnc_id": 26845,
"hgvs_c": "c.-319C>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": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.-107G>T",
"hgvs_p": null,
"transcript": "ENST00000593187.5",
"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": 299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.*84G>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
}
],
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"dbsnp": "rs138355894",
"frequency_reference_population": 6.841471e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84147e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.41629189252853394,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.181,
"revel_prediction": "Benign",
"alphamissense_score": 0.4411,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.969,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000245923.9",
"gene_symbol": "RTN2",
"hgnc_id": 10468,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1411G>T",
"hgvs_p": "p.Val471Leu"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000401705.5",
"gene_symbol": "PPM1N",
"hgnc_id": 26845,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-319C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}