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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: 3-119438024-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119438024&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 119438024,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018266.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "NM_018266.3",
"protein_id": "NP_060736.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 488,
"cds_start": 655,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 4853,
"mane_select": "ENST00000319172.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "ENST00000319172.10",
"protein_id": "ENSP00000326063.5",
"transcript_support_level": 1,
"aa_start": 219,
"aa_end": null,
"aa_length": 488,
"cds_start": 655,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 4853,
"mane_select": "NM_018266.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.*323G>A",
"hgvs_p": null,
"transcript": "ENST00000438581.6",
"protein_id": "ENSP00000402149.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.*323G>A",
"hgvs_p": null,
"transcript": "ENST00000438581.6",
"protein_id": "ENSP00000402149.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000491685.5",
"protein_id": "ENSP00000419641.1",
"transcript_support_level": 5,
"aa_start": 65,
"aa_end": null,
"aa_length": 164,
"cds_start": 193,
"cds_end": null,
"cds_length": 497,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "XM_006713687.3",
"protein_id": "XP_006713750.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 488,
"cds_start": 655,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 4809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "XM_017006788.3",
"protein_id": "XP_016862277.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 460,
"cds_start": 571,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 925,
"cdna_end": null,
"cdna_length": 4769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "XM_047448511.1",
"protein_id": "XP_047304467.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 460,
"cds_start": 571,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 4725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "XM_005247578.3",
"protein_id": "XP_005247635.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 377,
"cds_start": 655,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 4732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "XM_047448512.1",
"protein_id": "XP_047304468.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 377,
"cds_start": 655,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 4688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "XM_047448513.1",
"protein_id": "XP_047304469.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 349,
"cds_start": 571,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 925,
"cdna_end": null,
"cdna_length": 4648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile",
"transcript": "XM_011512958.4",
"protein_id": "XP_011511260.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 320,
"cds_start": 655,
"cds_end": null,
"cds_length": 963,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.736G>A",
"hgvs_p": null,
"transcript": "ENST00000486159.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.1118G>A",
"hgvs_p": null,
"transcript": "NR_073506.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.1009G>A",
"hgvs_p": null,
"transcript": "XR_007095705.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.-85G>A",
"hgvs_p": null,
"transcript": "ENST00000468545.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"dbsnp": "rs2080997807",
"frequency_reference_population": 0.0000012392526,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84139e-7,
"gnomad_genomes_af": 0.00000657099,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14240357279777527,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.027,
"revel_prediction": "Benign",
"alphamissense_score": 0.0788,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.055,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018266.3",
"gene_symbol": "TMEM39A",
"hgnc_id": 25600,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Ile"
}
],
"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
}