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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: 7-103540273-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=103540273&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 103540273,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005045.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu",
"transcript": "NM_005045.4",
"protein_id": "NP_005036.2",
"transcript_support_level": null,
"aa_start": 2285,
"aa_end": null,
"aa_length": 3460,
"cds_start": 6854,
"cds_end": null,
"cds_length": 10383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000428762.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005045.4"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu",
"transcript": "ENST00000428762.6",
"protein_id": "ENSP00000392423.1",
"transcript_support_level": 5,
"aa_start": 2285,
"aa_end": null,
"aa_length": 3460,
"cds_start": 6854,
"cds_end": null,
"cds_length": 10383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005045.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428762.6"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu",
"transcript": "ENST00000424685.3",
"protein_id": "ENSP00000388446.3",
"transcript_support_level": 5,
"aa_start": 2285,
"aa_end": null,
"aa_length": 3469,
"cds_start": 6854,
"cds_end": null,
"cds_length": 10410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424685.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu",
"transcript": "NM_173054.3",
"protein_id": "NP_774959.1",
"transcript_support_level": null,
"aa_start": 2285,
"aa_end": null,
"aa_length": 3458,
"cds_start": 6854,
"cds_end": null,
"cds_length": 10377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173054.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu",
"transcript": "ENST00000343529.9",
"protein_id": "ENSP00000345694.5",
"transcript_support_level": 5,
"aa_start": 2285,
"aa_end": null,
"aa_length": 3458,
"cds_start": 6854,
"cds_end": null,
"cds_length": 10377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343529.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.6738G>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000679867.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.646G>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000679952.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.6854G>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681034.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.734G>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000681315.1"
}
],
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"dbsnp": "rs116394157",
"frequency_reference_population": 0.00009603113,
"hom_count_reference_population": 0,
"allele_count_reference_population": 155,
"gnomad_exomes_af": 0.0000978191,
"gnomad_genomes_af": 0.000078855,
"gnomad_exomes_ac": 143,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7854015827178955,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.256,
"revel_prediction": "Benign",
"alphamissense_score": 0.4028,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.511,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005045.4",
"gene_symbol": "RELN",
"hgnc_id": 9957,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.6854G>T",
"hgvs_p": "p.Arg2285Leu"
}
],
"clinvar_disease": "Familial temporal lobe epilepsy 7,Norman-Roberts syndrome,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Familial temporal lobe epilepsy 7;Norman-Roberts syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}