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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: 2-165162732-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165162732&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165162732,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000283254.12",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "NM_006922.4",
"protein_id": "NP_008853.3",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 2000,
"cds_start": 791,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": "ENST00000283254.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000283254.12",
"protein_id": "ENSP00000283254.7",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 2000,
"cds_start": 791,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": "NM_006922.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000409101.7",
"protein_id": "ENSP00000386726.3",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 1951,
"cds_start": 791,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 6599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000706067.1",
"protein_id": "ENSP00000516211.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1983,
"cds_start": 791,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 1100,
"cdna_end": null,
"cdna_length": 8869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000639244.1",
"protein_id": "ENSP00000492251.1",
"transcript_support_level": 5,
"aa_start": 264,
"aa_end": null,
"aa_length": 1979,
"cds_start": 791,
"cds_end": null,
"cds_length": 5940,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 8854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "NM_001081676.2",
"protein_id": "NP_001075145.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1951,
"cds_start": 791,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 8955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "NM_001081677.2",
"protein_id": "NP_001075146.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1951,
"cds_start": 791,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 8955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000440431.6",
"protein_id": "ENSP00000403348.1",
"transcript_support_level": 5,
"aa_start": 264,
"aa_end": null,
"aa_length": 1363,
"cds_start": 791,
"cds_end": null,
"cds_length": 4092,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 4146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "ENST00000668657.1",
"protein_id": "ENSP00000499420.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1086,
"cds_start": 791,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 5424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_011511610.4",
"protein_id": "XP_011509912.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 2000,
"cds_start": 791,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1406,
"cdna_end": null,
"cdna_length": 9242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004660.3",
"protein_id": "XP_016860149.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 2000,
"cds_start": 791,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004661.3",
"protein_id": "XP_016860150.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1983,
"cds_start": 791,
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"cds_length": 5952,
"cdna_start": 1266,
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"cdna_length": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_047445394.1",
"protein_id": "XP_047301350.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1983,
"cds_start": 791,
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"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004662.3",
"protein_id": "XP_016860151.1",
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"mane_select": null,
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},
{
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"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": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_047445395.1",
"protein_id": "XP_047301351.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1257,
"cds_start": 791,
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"cdna_start": 1266,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004664.2",
"protein_id": "XP_016860153.1",
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"feature": null
},
{
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"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004665.2",
"protein_id": "XP_016860154.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1086,
"cds_start": 791,
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"cdna_start": 1266,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr",
"transcript": "XM_017004666.2",
"protein_id": "XP_016860155.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 1083,
"cds_start": 791,
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"cdna_start": 1266,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "n.791T>C",
"hgvs_p": null,
"transcript": "ENST00000638473.1",
"protein_id": "ENSP00000491552.1",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "n.791T>C",
"hgvs_p": null,
"transcript": "ENST00000640652.1",
"protein_id": "ENSP00000492807.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236283",
"gene_hgnc_id": null,
"hgvs_c": "n.321-32395A>G",
"hgvs_p": null,
"transcript": "ENST00000625505.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236283",
"gene_hgnc_id": null,
"hgvs_c": "n.643+23023A>G",
"hgvs_p": null,
"transcript": "ENST00000629817.2",
"protein_id": null,
"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": 980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"dbsnp": "rs768747448",
"frequency_reference_population": 0.000021889802,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000218898,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9168170690536499,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.953,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5353,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"phylop100way_prediction": "Pathogenic",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,PP5,BS2",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 4,
"pathogenic_score": 3,
"criteria": [
"PP3_Moderate",
"PP5",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000283254.12",
"gene_symbol": "SCN3A",
"hgnc_id": 10590,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.791T>C",
"hgvs_p": "p.Ile264Thr"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000625505.2",
"gene_symbol": "ENSG00000236283",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.321-32395A>G",
"hgvs_p": null
}
],
"clinvar_disease": " familial focal, with variable foci 4,Epilepsy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2",
"phenotype_combined": "not provided|Epilepsy, familial focal, with variable foci 4",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}