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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: 7-33021317-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=33021317&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 33021317,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000610140.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.395A>T",
"hgvs_p": "p.Asp132Val",
"transcript": "NM_001002010.5",
"protein_id": "NP_001002010.2",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 331,
"cds_start": 395,
"cds_end": null,
"cds_length": 996,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1667,
"mane_select": "ENST00000610140.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.395A>T",
"hgvs_p": "p.Asp132Val",
"transcript": "ENST00000610140.7",
"protein_id": "ENSP00000476480.2",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 331,
"cds_start": 395,
"cds_end": null,
"cds_length": 996,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1667,
"mane_select": "NM_001002010.5",
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "n.*300A>T",
"hgvs_p": null,
"transcript": "ENST00000456458.5",
"protein_id": "ENSP00000389676.2",
"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": 1742,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "n.*300A>T",
"hgvs_p": null,
"transcript": "ENST00000456458.5",
"protein_id": "ENSP00000389676.2",
"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": 1742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.296A>T",
"hgvs_p": "p.Asp99Val",
"transcript": "NM_001374335.1",
"protein_id": "NP_001361264.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 298,
"cds_start": 296,
"cds_end": null,
"cds_length": 897,
"cdna_start": 367,
"cdna_end": null,
"cdna_length": 1585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.293A>T",
"hgvs_p": "p.Asp98Val",
"transcript": "NM_001002009.3",
"protein_id": "NP_001002009.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 297,
"cds_start": 293,
"cds_end": null,
"cds_length": 894,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 1739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.293A>T",
"hgvs_p": "p.Asp98Val",
"transcript": "NM_016489.14",
"protein_id": "NP_057573.2",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 297,
"cds_start": 293,
"cds_end": null,
"cds_length": 894,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 1548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.293A>T",
"hgvs_p": "p.Asp98Val",
"transcript": "ENST00000643244.2",
"protein_id": "ENSP00000496364.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 297,
"cds_start": 293,
"cds_end": null,
"cds_length": 894,
"cdna_start": 341,
"cdna_end": null,
"cdna_length": 1559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "NM_001166118.3",
"protein_id": "NP_001159590.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 433,
"cdna_end": null,
"cdna_length": 1651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "NM_001356996.3",
"protein_id": "NP_001343925.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 1629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "NM_001374336.1",
"protein_id": "NP_001361265.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 602,
"cdna_end": null,
"cdna_length": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "NM_001374337.1",
"protein_id": "NP_001361266.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 292,
"cdna_end": null,
"cdna_length": 1510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "ENST00000409467.6",
"protein_id": "ENSP00000387166.1",
"transcript_support_level": 5,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 431,
"cdna_end": null,
"cdna_length": 1311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"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": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.395A>T",
"hgvs_p": "p.Asp132Val",
"transcript": "NM_001374338.1",
"protein_id": "NP_001361267.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 264,
"cds_start": 395,
"cds_end": null,
"cds_length": 795,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "NM_001374339.1",
"protein_id": "NP_001361268.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 264,
"cds_start": 194,
"cds_end": null,
"cds_length": 795,
"cdna_start": 422,
"cdna_end": null,
"cdna_length": 1640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"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": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.293A>T",
"hgvs_p": "p.Asp98Val",
"transcript": "ENST00000409787.4",
"protein_id": "ENSP00000387205.1",
"transcript_support_level": 2,
"aa_start": 98,
"aa_end": null,
"aa_length": 205,
"cds_start": 293,
"cds_end": null,
"cds_length": 618,
"cdna_start": 307,
"cdna_end": null,
"cdna_length": 840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"hgvs_c": "c.257A>T",
"hgvs_p": "p.Asp86Val",
"transcript": "XM_047420439.1",
"protein_id": "XP_047276395.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 285,
"cds_start": 257,
"cds_end": null,
"cds_length": 858,
"cdna_start": 607,
"cdna_end": null,
"cdna_length": 1825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NT5C3A",
"gene_hgnc_id": 17820,
"dbsnp": "rs104894025",
"frequency_reference_population": 0.000013645577,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000130132,
"gnomad_genomes_af": 0.0000197122,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9693077802658081,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.947,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.725,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.252,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.09,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000610140.7",
"gene_symbol": "NT5C3A",
"hgnc_id": 17820,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.395A>T",
"hgvs_p": "p.Asp132Val"
}
],
"clinvar_disease": "Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}