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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: 3-139373800-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=139373800&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 139373800,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000333188.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys",
"transcript": "NM_004766.3",
"protein_id": "NP_004757.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 906,
"cds_start": 760,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 3275,
"mane_select": "ENST00000333188.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys",
"transcript": "ENST00000333188.10",
"protein_id": "ENSP00000329419.4",
"transcript_support_level": 1,
"aa_start": 254,
"aa_end": null,
"aa_length": 906,
"cds_start": 760,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 3275,
"mane_select": "NM_004766.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys",
"transcript": "ENST00000503326.6",
"protein_id": "ENSP00000426682.2",
"transcript_support_level": 3,
"aa_start": 254,
"aa_end": null,
"aa_length": 904,
"cds_start": 760,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 4568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys",
"transcript": "ENST00000512309.2",
"protein_id": "ENSP00000422917.2",
"transcript_support_level": 5,
"aa_start": 254,
"aa_end": null,
"aa_length": 898,
"cds_start": 760,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 3373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Arg225Cys",
"transcript": "NM_001410834.1",
"protein_id": "NP_001397763.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 877,
"cds_start": 673,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 3701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Arg225Cys",
"transcript": "ENST00000507777.6",
"protein_id": "ENSP00000422295.1",
"transcript_support_level": 2,
"aa_start": 225,
"aa_end": null,
"aa_length": 877,
"cds_start": 673,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 803,
"cdna_end": null,
"cdna_length": 3221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Arg225Cys",
"transcript": "ENST00000512242.6",
"protein_id": "ENSP00000427185.2",
"transcript_support_level": 5,
"aa_start": 225,
"aa_end": null,
"aa_length": 877,
"cds_start": 673,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 1316,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Arg225Cys",
"transcript": "ENST00000514508.2",
"protein_id": "ENSP00000422469.2",
"transcript_support_level": 4,
"aa_start": 225,
"aa_end": null,
"aa_length": 877,
"cds_start": 673,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 3495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.526C>T",
"hgvs_p": "p.Arg176Cys",
"transcript": "ENST00000510181.6",
"protein_id": "ENSP00000502846.1",
"transcript_support_level": 2,
"aa_start": 176,
"aa_end": null,
"aa_length": 828,
"cds_start": 526,
"cds_end": null,
"cds_length": 2487,
"cdna_start": 1071,
"cdna_end": null,
"cdna_length": 3489,
"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": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.*722C>T",
"hgvs_p": null,
"transcript": "ENST00000677073.1",
"protein_id": "ENSP00000504033.1",
"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": 6872,
"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": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.785C>T",
"hgvs_p": null,
"transcript": "ENST00000677601.1",
"protein_id": "ENSP00000503393.1",
"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": 6770,
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.1547C>T",
"hgvs_p": null,
"transcript": "ENST00000677882.1",
"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": 12586,
"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": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.969C>T",
"hgvs_p": null,
"transcript": "NR_023350.1",
"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": 3202,
"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": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.*722C>T",
"hgvs_p": null,
"transcript": "ENST00000677073.1",
"protein_id": "ENSP00000504033.1",
"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": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "n.752-388C>T",
"hgvs_p": null,
"transcript": "ENST00000677309.1",
"protein_id": "ENSP00000503548.1",
"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": 6602,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"hgvs_c": "c.133-388C>T",
"hgvs_p": null,
"transcript": "XM_047449233.1",
"protein_id": "XP_047305189.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 652,
"cds_start": -4,
"cds_end": null,
"cds_length": 1959,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COPB2",
"gene_hgnc_id": 2232,
"dbsnp": "rs1229568621",
"frequency_reference_population": 0.00000805609,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000478894,
"gnomad_genomes_af": 0.0000394773,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8909717798233032,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.647,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8036,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.552,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000333188.10",
"gene_symbol": "COPB2",
"hgnc_id": 2232,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys"
}
],
"clinvar_disease": " autosomal recessive, primary,Microcephaly 19",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Microcephaly 19, primary, autosomal recessive",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}