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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: 1-230693393-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=230693393&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 230693393,
"ref": "A",
"alt": "G",
"effect": "stop_retained_variant",
"transcript": "ENST00000366669.9",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.2217A>G",
"hgvs_p": "p.Ter739Ter",
"transcript": "NM_007357.3",
"protein_id": "NP_031383.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 738,
"cds_start": 2217,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 2343,
"cdna_end": null,
"cdna_length": 2932,
"mane_select": "ENST00000366669.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.2217A>G",
"hgvs_p": "p.Ter739Ter",
"transcript": "ENST00000366669.9",
"protein_id": "ENSP00000355629.4",
"transcript_support_level": 1,
"aa_start": 739,
"aa_end": null,
"aa_length": 738,
"cds_start": 2217,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 2343,
"cdna_end": null,
"cdna_length": 2932,
"mane_select": "NM_007357.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.2214A>G",
"hgvs_p": "p.Ter738Ter",
"transcript": "ENST00000366668.7",
"protein_id": "ENSP00000355628.3",
"transcript_support_level": 1,
"aa_start": 738,
"aa_end": null,
"aa_length": 737,
"cds_start": 2214,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 2254,
"cdna_end": null,
"cdna_length": 2843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.2214A>G",
"hgvs_p": "p.Ter738Ter",
"transcript": "NM_001145036.2",
"protein_id": "NP_001138508.1",
"transcript_support_level": null,
"aa_start": 738,
"aa_end": null,
"aa_length": 737,
"cds_start": 2214,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 2340,
"cdna_end": null,
"cdna_length": 2929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.2040A>G",
"hgvs_p": "p.Ter680Ter",
"transcript": "ENST00000534989.1",
"protein_id": "ENSP00000440349.1",
"transcript_support_level": 2,
"aa_start": 680,
"aa_end": null,
"aa_length": 679,
"cds_start": 2040,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 2375,
"cdna_end": null,
"cdna_length": 2963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.1878A>G",
"hgvs_p": "p.Ter626Ter",
"transcript": "XM_047449445.1",
"protein_id": "XP_047305401.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 625,
"cds_start": 1878,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 1984,
"cdna_end": null,
"cdna_length": 2573,
"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": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "n.*2075A>G",
"hgvs_p": null,
"transcript": "ENST00000468893.6",
"protein_id": "ENSP00000476305.1",
"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": 2784,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.1254T>C",
"hgvs_p": null,
"transcript": "ENST00000657140.1",
"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": 2114,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*1991T>C",
"hgvs_p": null,
"transcript": "ENST00000679738.1",
"protein_id": "ENSP00000505063.1",
"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": 4894,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*2881T>C",
"hgvs_p": null,
"transcript": "ENST00000679802.1",
"protein_id": "ENSP00000505184.1",
"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": 5135,
"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": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.7727T>C",
"hgvs_p": null,
"transcript": "ENST00000679854.1",
"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": 8609,
"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": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.5528T>C",
"hgvs_p": null,
"transcript": "ENST00000681347.1",
"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": 6410,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*2916T>C",
"hgvs_p": null,
"transcript": "ENST00000681772.1",
"protein_id": "ENSP00000505829.1",
"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": 5410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "c.*1018T>C",
"hgvs_p": null,
"transcript": "ENST00000680783.1",
"protein_id": "ENSP00000506329.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 285,
"cds_start": -4,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5004,
"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": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "n.*2075A>G",
"hgvs_p": null,
"transcript": "ENST00000468893.6",
"protein_id": "ENSP00000476305.1",
"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": 2784,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*1991T>C",
"hgvs_p": null,
"transcript": "ENST00000679738.1",
"protein_id": "ENSP00000505063.1",
"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": 4894,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*2881T>C",
"hgvs_p": null,
"transcript": "ENST00000679802.1",
"protein_id": "ENSP00000505184.1",
"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": 5135,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGT",
"gene_hgnc_id": 333,
"hgvs_c": "n.*2916T>C",
"hgvs_p": null,
"transcript": "ENST00000681772.1",
"protein_id": "ENSP00000505829.1",
"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": 5410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"dbsnp": "rs1051038",
"frequency_reference_population": 0.23637359,
"hom_count_reference_population": 50880,
"allele_count_reference_population": 377161,
"gnomad_exomes_af": 0.234983,
"gnomad_genomes_af": 0.249566,
"gnomad_exomes_ac": 339184,
"gnomad_genomes_ac": 37977,
"gnomad_exomes_homalt": 45531,
"gnomad_genomes_homalt": 5349,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8600000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.86,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.761,
"phylop100way_prediction": "Benign",
"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": -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": "ENST00000366669.9",
"gene_symbol": "COG2",
"hgnc_id": 6546,
"effects": [
"stop_retained_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2217A>G",
"hgvs_p": "p.Ter739Ter"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000679738.1",
"gene_symbol": "AGT",
"hgnc_id": 333,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*1991T>C",
"hgvs_p": null
}
],
"clinvar_disease": " type IIq,Congenital disorder of glycosylation,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Congenital disorder of glycosylation, type IIq|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}