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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: 7-103539203-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=103539203&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 103539203,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000428762.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val",
"transcript": "NM_005045.4",
"protein_id": "NP_005036.2",
"transcript_support_level": null,
"aa_start": 2352,
"aa_end": null,
"aa_length": 3460,
"cds_start": 7055,
"cds_end": null,
"cds_length": 10383,
"cdna_start": 7357,
"cdna_end": null,
"cdna_length": 11708,
"mane_select": "ENST00000428762.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val",
"transcript": "ENST00000428762.6",
"protein_id": "ENSP00000392423.1",
"transcript_support_level": 5,
"aa_start": 2352,
"aa_end": null,
"aa_length": 3460,
"cds_start": 7055,
"cds_end": null,
"cds_length": 10383,
"cdna_start": 7357,
"cdna_end": null,
"cdna_length": 11708,
"mane_select": "NM_005045.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val",
"transcript": "ENST00000424685.3",
"protein_id": "ENSP00000388446.3",
"transcript_support_level": 5,
"aa_start": 2352,
"aa_end": null,
"aa_length": 3469,
"cds_start": 7055,
"cds_end": null,
"cds_length": 10410,
"cdna_start": 7215,
"cdna_end": null,
"cdna_length": 11683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val",
"transcript": "NM_173054.3",
"protein_id": "NP_774959.1",
"transcript_support_level": null,
"aa_start": 2352,
"aa_end": null,
"aa_length": 3458,
"cds_start": 7055,
"cds_end": null,
"cds_length": 10377,
"cdna_start": 7357,
"cdna_end": null,
"cdna_length": 11702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val",
"transcript": "ENST00000343529.9",
"protein_id": "ENSP00000345694.5",
"transcript_support_level": 5,
"aa_start": 2352,
"aa_end": null,
"aa_length": 3458,
"cds_start": 7055,
"cds_end": null,
"cds_length": 10377,
"cdna_start": 7215,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.296A>T",
"hgvs_p": null,
"transcript": "ENST00000478148.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 3081,
"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": 45,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.6939A>T",
"hgvs_p": null,
"transcript": "ENST00000679867.1",
"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": 14720,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.847A>T",
"hgvs_p": null,
"transcript": "ENST00000679952.1",
"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": 1899,
"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": 45,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.7055A>T",
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.935A>T",
"hgvs_p": null,
"transcript": "ENST00000681315.1",
"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": 1670,
"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": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.304A>T",
"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": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105375435",
"gene_hgnc_id": null,
"hgvs_c": "n.*110T>A",
"hgvs_p": null,
"transcript": "XR_001745315.2",
"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": 254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"dbsnp": "rs143688278",
"frequency_reference_population": 0.000023542152,
"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000246257,
"gnomad_genomes_af": 0.0000131373,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5649797916412354,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.22,
"revel_prediction": "Benign",
"alphamissense_score": 0.4418,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.911,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000428762.6",
"gene_symbol": "RELN",
"hgnc_id": 9957,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7055A>T",
"hgvs_p": "p.Asp2352Val"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_001745315.2",
"gene_symbol": "LOC105375435",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*110T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Familial temporal lobe epilepsy 7,Norman-Roberts syndrome,RELN-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Norman-Roberts syndrome;Familial temporal lobe epilepsy 7|RELN-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}