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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: 4-65495411-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=65495411&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 65495411,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000613740.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_001281766.3",
"protein_id": "NP_001268695.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 1016,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3051,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8345,
"mane_select": "ENST00000613740.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "ENST00000613740.5",
"protein_id": "ENSP00000478537.1",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 1016,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3051,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8345,
"mane_select": "NM_001281766.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "ENST00000622150.4",
"protein_id": "ENSP00000480763.1",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 1038,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3117,
"cdna_start": 1796,
"cdna_end": null,
"cdna_length": 8421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "ENST00000273854.7",
"protein_id": "ENSP00000273854.3",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 1037,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3114,
"cdna_start": 1644,
"cdna_end": null,
"cdna_length": 8266,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "ENST00000354839.8",
"protein_id": "ENSP00000346899.4",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1236,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "ENST00000511294.1",
"protein_id": "ENSP00000427638.1",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 1004,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 1796,
"cdna_end": null,
"cdna_length": 5176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_001281765.3",
"protein_id": "NP_001268694.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 1038,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3117,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_004439.8",
"protein_id": "NP_004430.4",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 1037,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3114,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_182472.5",
"protein_id": "NP_872272.2",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_001281767.3",
"protein_id": "NP_001268696.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 1004,
"cds_start": 1043,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 5173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Asp279Gly",
"transcript": "NM_001318761.2",
"protein_id": "NP_001305690.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 969,
"cds_start": 836,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 7535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "NM_001437319.1",
"protein_id": "NP_001424248.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 903,
"cds_start": 1043,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "XM_011531735.4",
"protein_id": "XP_011530037.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 926,
"cds_start": 1043,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly",
"transcript": "XM_017007878.3",
"protein_id": "XP_016863367.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 904,
"cds_start": 1043,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 1790,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.911-74846A>G",
"hgvs_p": null,
"transcript": "NM_001437313.1",
"protein_id": "NP_001424242.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": -4,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.911-74846A>G",
"hgvs_p": null,
"transcript": "ENST00000432638.6",
"protein_id": "ENSP00000389208.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": -4,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.911-74846A>G",
"hgvs_p": null,
"transcript": "NM_001437320.1",
"protein_id": "NP_001424249.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 873,
"cds_start": -4,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.911-74846A>G",
"hgvs_p": null,
"transcript": "NM_001437321.1",
"protein_id": "NP_001424250.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 852,
"cds_start": -4,
"cds_end": null,
"cds_length": 2559,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"hgvs_c": "c.911-74846A>G",
"hgvs_p": null,
"transcript": "XM_017007881.3",
"protein_id": "XP_016863370.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 817,
"cds_start": -4,
"cds_end": null,
"cds_length": 2454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPHA5",
"gene_hgnc_id": 3389,
"dbsnp": "rs200932017",
"frequency_reference_population": 0.000021691678,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000198455,
"gnomad_genomes_af": 0.000039413,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8530591726303101,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.658,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9944,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.585,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.11,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000613740.5",
"gene_symbol": "EPHA5",
"hgnc_id": 3389,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1043A>G",
"hgvs_p": "p.Asp348Gly"
}
],
"clinvar_disease": "Astrocytoma",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Astrocytoma",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}