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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: 22-18913355-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=18913355&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 18913355,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000357068.11",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1623C>T",
"hgvs_p": "p.Ala541Ala",
"transcript": "NM_016335.6",
"protein_id": "NP_057419.5",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 600,
"cds_start": 1623,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 1629,
"cdna_end": null,
"cdna_length": 2203,
"mane_select": "ENST00000357068.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1623C>T",
"hgvs_p": "p.Ala541Ala",
"transcript": "ENST00000357068.11",
"protein_id": "ENSP00000349577.6",
"transcript_support_level": 1,
"aa_start": 541,
"aa_end": null,
"aa_length": 600,
"cds_start": 1623,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 1629,
"cdna_end": null,
"cdna_length": 2203,
"mane_select": "NM_016335.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1623C>T",
"hgvs_p": "p.Ala541Ala",
"transcript": "ENST00000610940.4",
"protein_id": "ENSP00000480347.1",
"transcript_support_level": 1,
"aa_start": 541,
"aa_end": null,
"aa_length": 600,
"cds_start": 1623,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 1827,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1299C>T",
"hgvs_p": "p.Ala433Ala",
"transcript": "ENST00000334029.6",
"protein_id": "ENSP00000334726.2",
"transcript_support_level": 1,
"aa_start": 433,
"aa_end": null,
"aa_length": 492,
"cds_start": 1299,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 1985,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.4103C>T",
"hgvs_p": null,
"transcript": "ENST00000482858.5",
"protein_id": null,
"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": 4676,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.2532C>T",
"hgvs_p": null,
"transcript": "ENST00000491604.5",
"protein_id": null,
"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": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283809",
"gene_hgnc_id": null,
"hgvs_c": "c.513+2327G>A",
"hgvs_p": null,
"transcript": "ENST00000638240.1",
"protein_id": "ENSP00000492446.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": -4,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1299C>T",
"hgvs_p": "p.Ala433Ala",
"transcript": "NM_001195226.2",
"protein_id": "NP_001182155.2",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 492,
"cds_start": 1299,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 1514,
"cdna_end": null,
"cdna_length": 2088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1299C>T",
"hgvs_p": "p.Ala433Ala",
"transcript": "NM_001368250.2",
"protein_id": "NP_001355179.2",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 492,
"cds_start": 1299,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 1474,
"cdna_end": null,
"cdna_length": 2048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.1299C>T",
"hgvs_p": "p.Ala433Ala",
"transcript": "ENST00000420436.5",
"protein_id": "ENSP00000410805.1",
"transcript_support_level": 2,
"aa_start": 433,
"aa_end": null,
"aa_length": 492,
"cds_start": 1299,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 1460,
"cdna_end": null,
"cdna_length": 2034,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.2388C>T",
"hgvs_p": null,
"transcript": "ENST00000313755.9",
"protein_id": null,
"transcript_support_level": 2,
"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": 2961,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.1994C>T",
"hgvs_p": null,
"transcript": "ENST00000429300.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGCR6",
"gene_hgnc_id": 2846,
"hgvs_c": "n.*1997G>A",
"hgvs_p": null,
"transcript": "ENST00000483718.5",
"protein_id": "ENSP00000467483.1",
"transcript_support_level": 5,
"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": 3245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGCR6",
"gene_hgnc_id": 2846,
"hgvs_c": "n.*1997G>A",
"hgvs_p": null,
"transcript": "ENST00000483718.5",
"protein_id": "ENSP00000467483.1",
"transcript_support_level": 5,
"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": 3245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"dbsnp": "rs16983347",
"frequency_reference_population": 0.22607426,
"hom_count_reference_population": 2524,
"allele_count_reference_population": 5419,
"gnomad_exomes_af": 0.278359,
"gnomad_genomes_af": 0.226074,
"gnomad_exomes_ac": 86121,
"gnomad_genomes_ac": 5419,
"gnomad_exomes_homalt": 39173,
"gnomad_genomes_homalt": 2524,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.550000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.846,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000357068.11",
"gene_symbol": "PRODH",
"hgnc_id": 9453,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1623C>T",
"hgvs_p": "p.Ala541Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000638240.1",
"gene_symbol": "ENSG00000283809",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.513+2327G>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000483718.5",
"gene_symbol": "DGCR6",
"hgnc_id": 2846,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*1997G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Proline dehydrogenase deficiency,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Proline dehydrogenase deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}