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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: X-38401373-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=38401373&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 38401373,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000531.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "NM_000531.6",
"protein_id": "NP_000522.3",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000039007.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000531.6"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000039007.5",
"protein_id": "ENSP00000039007.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000531.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000039007.5"
},
{
"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": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250349",
"gene_hgnc_id": null,
"hgvs_c": "c.172-264748G>C",
"hgvs_p": null,
"transcript": "ENST00000465127.1",
"protein_id": "ENSP00000417050.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": null,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000465127.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "NM_001407092.1",
"protein_id": "NP_001394021.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001407092.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000713758.1",
"protein_id": "ENSP00000519059.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713758.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909233.1",
"protein_id": "ENSP00000579292.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909233.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909234.1",
"protein_id": "ENSP00000579293.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 354,
"cds_start": 485,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909234.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909238.1",
"protein_id": "ENSP00000579297.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 350,
"cds_start": 485,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909238.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.461G>C",
"hgvs_p": "p.Gly154Ala",
"transcript": "ENST00000909240.1",
"protein_id": "ENSP00000579299.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 346,
"cds_start": 461,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909240.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909239.1",
"protein_id": "ENSP00000579298.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 336,
"cds_start": 485,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909239.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909241.1",
"protein_id": "ENSP00000579300.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 336,
"cds_start": 485,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909241.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909236.1",
"protein_id": "ENSP00000579295.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 313,
"cds_start": 485,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909236.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909235.1",
"protein_id": "ENSP00000579294.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 308,
"cds_start": 485,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909235.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.320G>C",
"hgvs_p": "p.Gly107Ala",
"transcript": "ENST00000713759.1",
"protein_id": "ENSP00000519060.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 299,
"cds_start": 320,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713759.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "ENST00000909237.1",
"protein_id": "ENSP00000579296.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 245,
"cds_start": 485,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909237.1"
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala",
"transcript": "XM_017029556.2",
"protein_id": "XP_016885045.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 311,
"cds_start": 485,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029556.2"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.522G>C",
"hgvs_p": null,
"transcript": "ENST00000488812.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000488812.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*235G>C",
"hgvs_p": null,
"transcript": "ENST00000643344.1",
"protein_id": "ENSP00000496606.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000643344.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*247G>C",
"hgvs_p": null,
"transcript": "ENST00000713760.1",
"protein_id": "ENSP00000519061.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000713760.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*235G>C",
"hgvs_p": null,
"transcript": "ENST00000643344.1",
"protein_id": "ENSP00000496606.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000643344.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*247G>C",
"hgvs_p": null,
"transcript": "ENST00000713760.1",
"protein_id": "ENSP00000519061.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000713760.1"
}
],
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"dbsnp": "rs72556272",
"frequency_reference_population": 9.165609e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.16561e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9767966270446777,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.812,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3275,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.543,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000531.6",
"gene_symbol": "OTC",
"hgnc_id": 8512,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.485G>C",
"hgvs_p": "p.Gly162Ala"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000465127.1",
"gene_symbol": "ENSG00000250349",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.172-264748G>C",
"hgvs_p": null
}
],
"clinvar_disease": "OTC-related disorder,Ornithine carbamoyltransferase deficiency,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "Ornithine carbamoyltransferase deficiency|OTC-related disorder|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}