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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: 5-81207283-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=81207283&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 81207283,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006909.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.3005C>T",
"hgvs_p": "p.Ser1002Leu",
"transcript": "NM_006909.3",
"protein_id": "NP_008840.1",
"transcript_support_level": null,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3005,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265080.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006909.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.3005C>T",
"hgvs_p": "p.Ser1002Leu",
"transcript": "ENST00000265080.9",
"protein_id": "ENSP00000265080.4",
"transcript_support_level": 1,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3005,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006909.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265080.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "n.3005C>T",
"hgvs_p": null,
"transcript": "ENST00000503795.1",
"protein_id": "ENSP00000421771.1",
"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": "ENST00000503795.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.2960C>T",
"hgvs_p": "p.Ser987Leu",
"transcript": "ENST00000933988.1",
"protein_id": "ENSP00000604047.1",
"transcript_support_level": null,
"aa_start": 987,
"aa_end": null,
"aa_length": 1222,
"cds_start": 2960,
"cds_end": null,
"cds_length": 3669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933988.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.2633C>T",
"hgvs_p": "p.Ser878Leu",
"transcript": "XM_047417463.1",
"protein_id": "XP_047273419.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 1113,
"cds_start": 2633,
"cds_end": null,
"cds_length": 3342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417463.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.2633C>T",
"hgvs_p": "p.Ser878Leu",
"transcript": "XM_047417464.1",
"protein_id": "XP_047273420.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 1113,
"cds_start": 2633,
"cds_end": null,
"cds_length": 3342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417464.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.2576C>T",
"hgvs_p": "p.Ser859Leu",
"transcript": "XM_047417465.1",
"protein_id": "XP_047273421.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2576,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417465.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"hgvs_c": "c.2576C>T",
"hgvs_p": "p.Ser859Leu",
"transcript": "XM_047417466.1",
"protein_id": "XP_047273422.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2576,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417466.1"
},
{
"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": "LOC124901017",
"gene_hgnc_id": null,
"hgvs_c": "n.3008G>A",
"hgvs_p": null,
"transcript": "XR_007058842.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007058842.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "CKMT2-AS1",
"gene_hgnc_id": 48997,
"hgvs_c": "n.333-2960G>A",
"hgvs_p": null,
"transcript": "ENST00000503483.6",
"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": "ENST00000503483.6"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKMT2-AS1",
"gene_hgnc_id": 48997,
"hgvs_c": "n.187-3756G>A",
"hgvs_p": null,
"transcript": "ENST00000663674.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000663674.1"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CKMT2-AS1",
"gene_hgnc_id": 48997,
"hgvs_c": "n.622-405G>A",
"hgvs_p": null,
"transcript": "ENST00000793747.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000793747.1"
}
],
"gene_symbol": "RASGRF2",
"gene_hgnc_id": 9876,
"dbsnp": "rs747408294",
"frequency_reference_population": 0.000083644576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 135,
"gnomad_exomes_af": 0.0000875603,
"gnomad_genomes_af": 0.0000460157,
"gnomad_exomes_ac": 128,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8212688565254211,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.365,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3446,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006909.3",
"gene_symbol": "RASGRF2",
"hgnc_id": 9876,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3005C>T",
"hgvs_p": "p.Ser1002Leu"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007058842.1",
"gene_symbol": "LOC124901017",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3008G>A",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000503483.6",
"gene_symbol": "CKMT2-AS1",
"hgnc_id": 48997,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.333-2960G>A",
"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
}