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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: 19-45488954-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45488954&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RTN2",
"hgnc_id": 10468,
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425Gln",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_005619.5",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"gene_symbol": "PPM1N",
"hgnc_id": 26845,
"hgvs_c": "c.-41C>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000401705.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 557,
"alphamissense_prediction": null,
"alphamissense_score": 0.0788,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "19",
"clinvar_classification": "Benign",
"clinvar_disease": "Spastic paraplegia,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0033495426177978516,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 545,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": 1496,
"cds_end": null,
"cds_length": 1638,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_005619.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000245923.9",
"protein_coding": true,
"protein_id": "NP_005610.1",
"strand": false,
"transcript": "NM_005619.5",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 545,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": 1496,
"cds_end": null,
"cds_length": 1638,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000245923.9",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005619.5",
"protein_coding": true,
"protein_id": "ENSP00000245923.3",
"strand": false,
"transcript": "ENST00000245923.9",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 472,
"aa_ref": "R",
"aa_start": 352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2063,
"cdna_start": 1285,
"cds_end": null,
"cds_length": 1419,
"cds_start": 1055,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000344680.8",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.1055G>A",
"hgvs_p": "p.Arg352Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000345127.3",
"strand": false,
"transcript": "ENST00000344680.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 205,
"aa_ref": "R",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1127,
"cdna_start": 349,
"cds_end": null,
"cds_length": 618,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000430715.6",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.254G>A",
"hgvs_p": "p.Arg85Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398178.1",
"strand": false,
"transcript": "ENST00000430715.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2111,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000591286.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.*272G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467863.1",
"strand": false,
"transcript": "ENST00000591286.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2111,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000591286.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.*272G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467863.1",
"strand": false,
"transcript": "ENST00000591286.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 112,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 771,
"cdna_start": null,
"cds_end": null,
"cds_length": 339,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000401705.5",
"gene_hgnc_id": 26845,
"gene_symbol": "PPM1N",
"hgvs_c": "c.-41C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384318.1",
"strand": true,
"transcript": "ENST00000401705.5",
"transcript_support_level": 3
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 472,
"aa_ref": "R",
"aa_start": 352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2055,
"cdna_start": 1277,
"cds_end": null,
"cds_length": 1419,
"cds_start": 1055,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_206900.3",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.1055G>A",
"hgvs_p": "p.Arg352Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_996783.1",
"strand": false,
"transcript": "NM_206900.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 470,
"aa_ref": "R",
"aa_start": 352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2005,
"cdna_start": 1233,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1055,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000920224.1",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.1055G>A",
"hgvs_p": "p.Arg352Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590283.1",
"strand": false,
"transcript": "ENST00000920224.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 271,
"aa_ref": "R",
"aa_start": 151,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2357,
"cdna_start": 1579,
"cds_end": null,
"cds_length": 816,
"cds_start": 452,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000590526.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.452G>A",
"hgvs_p": "p.Arg151Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466619.1",
"strand": false,
"transcript": "ENST00000590526.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 205,
"aa_ref": "R",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1113,
"cdna_start": 335,
"cds_end": null,
"cds_length": 618,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_206901.3",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "c.254G>A",
"hgvs_p": "p.Arg85Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_996784.1",
"strand": false,
"transcript": "NM_206901.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 112,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 771,
"cdna_start": null,
"cds_end": null,
"cds_length": 339,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000401705.5",
"gene_hgnc_id": 26845,
"gene_symbol": "PPM1N",
"hgvs_c": "c.-41C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384318.1",
"strand": true,
"transcript": "ENST00000401705.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2212,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000587597.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.1274G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468144.1",
"strand": false,
"transcript": "ENST00000587597.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 546,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000588036.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.112G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000588036.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 435,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000589628.1",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.241G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000589628.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 682,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000591789.1",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.20G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000591789.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 526,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000593129.1",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.150G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000593129.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000590746.5",
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"hgvs_c": "n.62-2841G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590746.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs35461805",
"effect": "missense_variant",
"frequency_reference_population": 0.00034560982,
"gene_hgnc_id": 10468,
"gene_symbol": "RTN2",
"gnomad_exomes_ac": 305,
"gnomad_exomes_af": 0.00020899,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 252,
"gnomad_genomes_af": 0.00165522,
"gnomad_genomes_homalt": 2,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Spastic paraplegia|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.276,
"pos": 45488954,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.04,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_005619.5"
}
]
}