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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: 3-149178609-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149178609&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 149178609,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000096.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "NM_000096.4",
"protein_id": "NP_000087.2",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": "ENST00000264613.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "ENST00000264613.11",
"protein_id": "ENSP00000264613.6",
"transcript_support_level": 1,
"aa_start": 895,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": "NM_000096.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2033G>C",
"hgvs_p": "p.Gly678Ala",
"transcript": "ENST00000494544.1",
"protein_id": "ENSP00000420545.1",
"transcript_support_level": 1,
"aa_start": 678,
"aa_end": null,
"aa_length": 852,
"cds_start": 2033,
"cds_end": null,
"cds_length": 2559,
"cdna_start": 2033,
"cdna_end": null,
"cdna_length": 2806,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.601G>C",
"hgvs_p": null,
"transcript": "ENST00000460674.5",
"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": 2269,
"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": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.2716G>C",
"hgvs_p": null,
"transcript": "ENST00000490639.5",
"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": 3105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.89G>C",
"hgvs_p": "p.Gly30Ala",
"transcript": "ENST00000479771.5",
"protein_id": "ENSP00000420367.1",
"transcript_support_level": 5,
"aa_start": 30,
"aa_end": null,
"aa_length": 225,
"cds_start": 89,
"cds_end": null,
"cds_length": 678,
"cdna_start": 89,
"cdna_end": null,
"cdna_length": 1150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_011512435.3",
"protein_id": "XP_011510737.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 3797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_006713499.4",
"protein_id": "XP_006713562.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1090,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3273,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 3785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_006713500.5",
"protein_id": "XP_006713563.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3210,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 4464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_017005734.3",
"protein_id": "XP_016861223.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3210,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 5420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_006713501.4",
"protein_id": "XP_006713564.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 5511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala",
"transcript": "XM_017005735.3",
"protein_id": "XP_016861224.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2684,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 4289,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.206G>C",
"hgvs_p": null,
"transcript": "ENST00000463556.5",
"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": 590,
"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": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.2471G>C",
"hgvs_p": null,
"transcript": "ENST00000481169.5",
"protein_id": "ENSP00000418773.1",
"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": 3411,
"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": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.2508G>C",
"hgvs_p": null,
"transcript": "NR_046371.2",
"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": 3409,
"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": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.2721G>C",
"hgvs_p": null,
"transcript": "XR_427361.4",
"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": 3622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"dbsnp": "rs139633388",
"frequency_reference_population": 0.0018241314,
"hom_count_reference_population": 3,
"allele_count_reference_population": 2940,
"gnomad_exomes_af": 0.00185159,
"gnomad_genomes_af": 0.00156024,
"gnomad_exomes_ac": 2703,
"gnomad_genomes_ac": 237,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14648741483688354,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.947,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.555,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 6,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000096.4",
"gene_symbol": "CP",
"hgnc_id": 2295,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2684G>C",
"hgvs_p": "p.Gly895Ala"
}
],
"clinvar_disease": "CP-related disorder,Deficiency of ferroxidase,Hypoceruloplasminemia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:8 LB:3",
"phenotype_combined": "Deficiency of ferroxidase|not specified|not provided|Hypoceruloplasminemia|CP-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}