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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: 2-46758656-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=46758656&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 46758656,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_014011.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "NM_144949.3",
"protein_id": "NP_659198.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 4766,
"mane_select": "ENST00000394861.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144949.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000394861.3",
"protein_id": "ENSP00000378330.2",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 4766,
"mane_select": "NM_144949.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394861.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000306503.5",
"protein_id": "ENSP00000305133.5",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 4771,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000306503.5"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "NM_014011.5",
"protein_id": "NP_054730.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 313,
"cdna_end": null,
"cdna_length": 4786,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014011.5"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000861862.1",
"protein_id": "ENSP00000531921.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 215,
"cdna_end": null,
"cdna_length": 4230,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861862.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000861863.1",
"protein_id": "ENSP00000531922.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 450,
"cdna_end": null,
"cdna_length": 4096,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861863.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000861864.1",
"protein_id": "ENSP00000531923.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 309,
"cdna_end": null,
"cdna_length": 4319,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861864.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000861865.1",
"protein_id": "ENSP00000531924.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 335,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861865.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000929596.1",
"protein_id": "ENSP00000599655.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 4471,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929596.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000929597.1",
"protein_id": "ENSP00000599656.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 275,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929597.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000952072.1",
"protein_id": "ENSP00000622131.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 379,
"cdna_end": null,
"cdna_length": 2518,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952072.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp",
"transcript": "ENST00000952073.1",
"protein_id": "ENSP00000622132.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 536,
"cds_start": 126,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 189,
"cdna_end": null,
"cdna_length": 4198,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952073.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01118",
"gene_hgnc_id": 49261,
"hgvs_c": "n.173-38663G>C",
"hgvs_p": null,
"transcript": "ENST00000650611.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1992,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000650611.2"
}
],
"gene_symbol": "SOCS5",
"gene_hgnc_id": 16852,
"dbsnp": "rs150807217",
"frequency_reference_population": 0.00017408888,
"hom_count_reference_population": 0,
"allele_count_reference_population": 281,
"gnomad_exomes_af": 0.000096454,
"gnomad_genomes_af": 0.000919347,
"gnomad_exomes_ac": 141,
"gnomad_genomes_ac": 140,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004136443138122559,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": 0.0739,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.014,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_014011.5",
"gene_symbol": "SOCS5",
"hgnc_id": 16852,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.126G>C",
"hgvs_p": "p.Glu42Asp"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000650611.2",
"gene_symbol": "LINC01118",
"hgnc_id": 49261,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.173-38663G>C",
"hgvs_p": null
}
],
"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
}