← Back to variant description
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: 2-165367225-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165367225&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165367225,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000283256.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "NM_001040142.2",
"protein_id": "NP_001035232.1",
"transcript_support_level": null,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3807,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "ENST00000375437.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "NM_001371246.1",
"protein_id": "NP_001358175.1",
"transcript_support_level": null,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3807,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "ENST00000631182.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "ENST00000375437.7",
"protein_id": "ENSP00000364586.2",
"transcript_support_level": 5,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3807,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "NM_001040142.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "ENST00000631182.3",
"protein_id": "ENSP00000486885.1",
"transcript_support_level": 5,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3807,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "NM_001371246.1",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "ENST00000283256.10",
"protein_id": "ENSP00000283256.6",
"transcript_support_level": 1,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3685,
"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": 19,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.3672C>T",
"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": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "NM_001040143.2",
"protein_id": "NP_001035233.1",
"transcript_support_level": null,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3926,
"cdna_end": null,
"cdna_length": 8895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "NM_001371247.1",
"protein_id": "NP_001358176.1",
"transcript_support_level": null,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3635,
"cdna_end": null,
"cdna_length": 8604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "NM_021007.3",
"protein_id": "NP_066287.2",
"transcript_support_level": null,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3661,
"cdna_end": null,
"cdna_length": 8630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "ENST00000636071.2",
"protein_id": "ENSP00000490107.1",
"transcript_support_level": 5,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3906,
"cdna_end": null,
"cdna_length": 8881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp",
"transcript": "ENST00000637266.2",
"protein_id": "ENSP00000490866.1",
"transcript_support_level": 5,
"aa_start": 1177,
"aa_end": null,
"aa_length": 2005,
"cds_start": 3529,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 3635,
"cdna_end": null,
"cdna_length": 8610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.3133C>T",
"hgvs_p": "p.Arg1045Trp",
"transcript": "ENST00000636985.2",
"protein_id": "ENSP00000490849.1",
"transcript_support_level": 5,
"aa_start": 1045,
"aa_end": null,
"aa_length": 1873,
"cds_start": 3133,
"cds_end": null,
"cds_length": 5622,
"cdna_start": 3881,
"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": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1848C>T",
"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": 21,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1516C>T",
"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": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*4052C>T",
"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": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1471C>T",
"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": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1848C>T",
"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": 21,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1516C>T",
"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": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*4052C>T",
"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": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.*1471C>T",
"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": "rs115231482",
"frequency_reference_population": 0.000104093735,
"hom_count_reference_population": 0,
"allele_count_reference_population": 168,
"gnomad_exomes_af": 0.000108088,
"gnomad_genomes_af": 0.0000657229,
"gnomad_exomes_ac": 158,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6022775173187256,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.583,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1575,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.471,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Likely_benign",
"acmg_criteria": "PP2,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000283256.10",
"gene_symbol": "SCN2A",
"hgnc_id": 10588,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3529C>T",
"hgvs_p": "p.Arg1177Trp"
}
],
"clinvar_disease": " 11, 3, benign familial infantile, type 9,Developmental and epileptic encephalopathy,Episodic ataxia,Genetic developmental and epileptic encephalopathy,Inborn genetic diseases,Seizures,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|not provided|Inborn genetic diseases|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11;Episodic ataxia, type 9|Genetic developmental and epileptic encephalopathy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}