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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: 2-165388750-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165388750&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165388750,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001040142.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "NM_001040142.2",
"protein_id": "NP_001035232.1",
"transcript_support_level": null,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5222,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "ENST00000375437.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "NM_001371246.1",
"protein_id": "NP_001358175.1",
"transcript_support_level": null,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5222,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "ENST00000631182.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "ENST00000375437.7",
"protein_id": "ENSP00000364586.2",
"transcript_support_level": 5,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5222,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "NM_001040142.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "ENST00000631182.3",
"protein_id": "ENSP00000486885.1",
"transcript_support_level": 5,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5222,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "NM_001371246.1",
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "ENST00000283256.10",
"protein_id": "ENSP00000283256.6",
"transcript_support_level": 1,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5100,
"cdna_end": null,
"cdna_length": 8660,
"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": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.8375G>A",
"hgvs_p": null,
"transcript": "ENST00000480032.4",
"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": 11676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "NM_001040143.2",
"protein_id": "NP_001035233.1",
"transcript_support_level": null,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5341,
"cdna_end": null,
"cdna_length": 8895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "NM_001371247.1",
"protein_id": "NP_001358176.1",
"transcript_support_level": null,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5050,
"cdna_end": null,
"cdna_length": 8604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "NM_021007.3",
"protein_id": "NP_066287.2",
"transcript_support_level": null,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5076,
"cdna_end": null,
"cdna_length": 8630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "ENST00000636071.2",
"protein_id": "ENSP00000490107.1",
"transcript_support_level": 5,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5321,
"cdna_end": null,
"cdna_length": 8881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr",
"transcript": "ENST00000637266.2",
"protein_id": "ENSP00000490866.1",
"transcript_support_level": 5,
"aa_start": 1648,
"aa_end": null,
"aa_length": 2005,
"cds_start": 4944,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 5050,
"cdna_end": null,
"cdna_length": 8610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.4548G>A",
"hgvs_p": "p.Thr1516Thr",
"transcript": "ENST00000636985.2",
"protein_id": "ENSP00000490849.1",
"transcript_support_level": 5,
"aa_start": 1516,
"aa_end": null,
"aa_length": 1873,
"cds_start": 4548,
"cds_end": null,
"cds_length": 5622,
"cdna_start": 5296,
"cdna_end": null,
"cdna_length": 8856,
"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": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*3263G>A",
"hgvs_p": null,
"transcript": "ENST00000636135.1",
"protein_id": "ENSP00000489821.1",
"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": 8519,
"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": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*2931G>A",
"hgvs_p": null,
"transcript": "ENST00000636384.2",
"protein_id": "ENSP00000490765.1",
"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": 9007,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*5467G>A",
"hgvs_p": null,
"transcript": "ENST00000636662.2",
"protein_id": "ENSP00000489873.1",
"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": 9456,
"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": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*2886G>A",
"hgvs_p": null,
"transcript": "ENST00000636769.1",
"protein_id": "ENSP00000490800.1",
"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": 8573,
"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": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*3263G>A",
"hgvs_p": null,
"transcript": "ENST00000636135.1",
"protein_id": "ENSP00000489821.1",
"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": 8519,
"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": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*2931G>A",
"hgvs_p": null,
"transcript": "ENST00000636384.2",
"protein_id": "ENSP00000490765.1",
"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": 9007,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*5467G>A",
"hgvs_p": null,
"transcript": "ENST00000636662.2",
"protein_id": "ENSP00000489873.1",
"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": 9456,
"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": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*2886G>A",
"hgvs_p": null,
"transcript": "ENST00000636769.1",
"protein_id": "ENSP00000490800.1",
"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": 8573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"dbsnp": "rs565309819",
"frequency_reference_population": 0.00012329464,
"hom_count_reference_population": 3,
"allele_count_reference_population": 199,
"gnomad_exomes_af": 0.000128609,
"gnomad_genomes_af": 0.00007226,
"gnomad_exomes_ac": 188,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"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": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.251,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001040142.2",
"gene_symbol": "SCN2A",
"hgnc_id": 10588,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4944G>A",
"hgvs_p": "p.Thr1648Thr"
}
],
"clinvar_disease": " 11, 3, benign familial infantile,Developmental and epileptic encephalopathy,Seizures,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "not specified|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}