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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: 19-45494800-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45494800&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45494800,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_005619.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu",
"transcript": "NM_005619.5",
"protein_id": "NP_005610.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 545,
"cds_start": 285,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000245923.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005619.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu",
"transcript": "ENST00000245923.9",
"protein_id": "ENSP00000245923.3",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 545,
"cds_start": 285,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005619.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000245923.9"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu",
"transcript": "ENST00000344680.8",
"protein_id": "ENSP00000345127.3",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 472,
"cds_start": 285,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000344680.8"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.285A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000591286.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu",
"transcript": "NM_206900.3",
"protein_id": "NP_996783.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 472,
"cds_start": 285,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_206900.3"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu",
"transcript": "ENST00000920224.1",
"protein_id": "ENSP00000590283.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 470,
"cds_start": 285,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920224.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "c.-538A>G",
"hgvs_p": null,
"transcript": "ENST00000590526.5",
"protein_id": "ENSP00000466619.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": null,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590526.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PPM1N",
"gene_hgnc_id": 26845,
"hgvs_c": "c.-15-5149T>C",
"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": null,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000401705.5"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.285A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000587597.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"hgvs_c": "n.344A>G",
"hgvs_p": null,
"transcript": "ENST00000589384.1",
"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": "ENST00000589384.1"
},
{
"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.106A>G",
"hgvs_p": null,
"transcript": "ENST00000592064.1",
"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": "ENST00000592064.1"
}
],
"gene_symbol": "RTN2",
"gene_hgnc_id": 10468,
"dbsnp": "rs146004780",
"frequency_reference_population": 0.00066187774,
"hom_count_reference_population": 10,
"allele_count_reference_population": 1062,
"gnomad_exomes_af": 0.000365642,
"gnomad_genomes_af": 0.00348686,
"gnomad_exomes_ac": 531,
"gnomad_genomes_ac": 531,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 6,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.04,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005619.5",
"gene_symbol": "RTN2",
"hgnc_id": 10468,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.285A>G",
"hgvs_p": "p.Glu95Glu"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000401705.5",
"gene_symbol": "PPM1N",
"hgnc_id": 26845,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-15-5149T>C",
"hgvs_p": null
}
],
"clinvar_disease": "RTN2-related disorder,Spastic paraplegia,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Spastic paraplegia|not provided|RTN2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}