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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: 7-103472873-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=103472873&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 103472873,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000428762.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.10322G>A",
"hgvs_p": "p.Arg3441Gln",
"transcript": "NM_005045.4",
"protein_id": "NP_005036.2",
"transcript_support_level": null,
"aa_start": 3441,
"aa_end": null,
"aa_length": 3460,
"cds_start": 10322,
"cds_end": null,
"cds_length": 10383,
"cdna_start": 10624,
"cdna_end": null,
"cdna_length": 11708,
"mane_select": "ENST00000428762.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.10322G>A",
"hgvs_p": "p.Arg3441Gln",
"transcript": "ENST00000428762.6",
"protein_id": "ENSP00000392423.1",
"transcript_support_level": 5,
"aa_start": 3441,
"aa_end": null,
"aa_length": 3460,
"cds_start": 10322,
"cds_end": null,
"cds_length": 10383,
"cdna_start": 10624,
"cdna_end": null,
"cdna_length": 11708,
"mane_select": "NM_005045.4",
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A5-AS1",
"gene_hgnc_id": 55680,
"hgvs_c": "n.1365+26205C>T",
"hgvs_p": null,
"transcript": "ENST00000422488.1",
"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": 2725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.10316G>A",
"hgvs_p": "p.Arg3439Gln",
"transcript": "NM_173054.3",
"protein_id": "NP_774959.1",
"transcript_support_level": null,
"aa_start": 3439,
"aa_end": null,
"aa_length": 3458,
"cds_start": 10316,
"cds_end": null,
"cds_length": 10377,
"cdna_start": 10618,
"cdna_end": null,
"cdna_length": 11702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.10316G>A",
"hgvs_p": "p.Arg3439Gln",
"transcript": "ENST00000343529.9",
"protein_id": "ENSP00000345694.5",
"transcript_support_level": 5,
"aa_start": 3439,
"aa_end": null,
"aa_length": 3458,
"cds_start": 10316,
"cds_end": null,
"cds_length": 10377,
"cdna_start": 10476,
"cdna_end": null,
"cdna_length": 11565,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.*109G>A",
"hgvs_p": null,
"transcript": "ENST00000429186.2",
"protein_id": "ENSP00000404818.2",
"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": 1419,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.2073G>A",
"hgvs_p": null,
"transcript": "ENST00000679371.1",
"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": 3565,
"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": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.3868G>A",
"hgvs_p": null,
"transcript": "ENST00000680248.1",
"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": 5352,
"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": 66,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.*125G>A",
"hgvs_p": null,
"transcript": "ENST00000681034.1",
"protein_id": "ENSP00000506075.1",
"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": 11763,
"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": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.3565G>A",
"hgvs_p": null,
"transcript": "ENST00000681364.1",
"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": 5049,
"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": 65,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.*42G>A",
"hgvs_p": null,
"transcript": "ENST00000424685.3",
"protein_id": "ENSP00000388446.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 3469,
"cds_start": -4,
"cds_end": null,
"cds_length": 10410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11683,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.*109G>A",
"hgvs_p": null,
"transcript": "ENST00000429186.2",
"protein_id": "ENSP00000404818.2",
"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": 1419,
"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": 66,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.*125G>A",
"hgvs_p": null,
"transcript": "ENST00000681034.1",
"protein_id": "ENSP00000506075.1",
"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": 11763,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A5-AS1",
"gene_hgnc_id": 55680,
"hgvs_c": "n.307+26205C>T",
"hgvs_p": null,
"transcript": "ENST00000660729.1",
"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": 1193,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A5-AS1",
"gene_hgnc_id": 55680,
"hgvs_c": "n.292+26205C>T",
"hgvs_p": null,
"transcript": "ENST00000841470.1",
"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": 965,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A5-AS1",
"gene_hgnc_id": 55680,
"hgvs_c": "n.305-17305C>T",
"hgvs_p": null,
"transcript": "ENST00000841471.1",
"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": 1191,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A5-AS1",
"gene_hgnc_id": 55680,
"hgvs_c": "n.1365+26205C>T",
"hgvs_p": null,
"transcript": "NR_110141.1",
"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": 2725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"dbsnp": "rs116463039",
"frequency_reference_population": 0.0000551518,
"hom_count_reference_population": 0,
"allele_count_reference_population": 89,
"gnomad_exomes_af": 0.0000492625,
"gnomad_genomes_af": 0.000111717,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.16651377081871033,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.484,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2134,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.466,
"phylop100way_prediction": "Uncertain_significance",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000428762.6",
"gene_symbol": "RELN",
"hgnc_id": 9957,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.10322G>A",
"hgvs_p": "p.Arg3441Gln"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000422488.1",
"gene_symbol": "SLC26A5-AS1",
"hgnc_id": 55680,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1365+26205C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 1, familial temporal lobe,Epilepsy,Familial temporal lobe epilepsy 7,Norman-Roberts syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 B:1",
"phenotype_combined": "Norman-Roberts syndrome|Norman-Roberts syndrome;Familial temporal lobe epilepsy 7|Norman-Roberts syndrome;Familial temporal lobe epilepsy 7;Epilepsy, familial temporal lobe, 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}