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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: 7-103489775-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=103489775&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 103489775,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005045.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg",
"transcript": "NM_005045.4",
"protein_id": "NP_005036.2",
"transcript_support_level": null,
"aa_start": 3244,
"aa_end": null,
"aa_length": 3460,
"cds_start": 9730,
"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": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg",
"transcript": "ENST00000428762.6",
"protein_id": "ENSP00000392423.1",
"transcript_support_level": 5,
"aa_start": 3244,
"aa_end": null,
"aa_length": 3460,
"cds_start": 9730,
"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": 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.1366-14629C>G",
"hgvs_p": null,
"transcript": "ENST00000422488.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000422488.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg",
"transcript": "ENST00000424685.3",
"protein_id": "ENSP00000388446.3",
"transcript_support_level": 5,
"aa_start": 3244,
"aa_end": null,
"aa_length": 3469,
"cds_start": 9730,
"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": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg",
"transcript": "NM_173054.3",
"protein_id": "NP_774959.1",
"transcript_support_level": null,
"aa_start": 3244,
"aa_end": null,
"aa_length": 3458,
"cds_start": 9730,
"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": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg",
"transcript": "ENST00000343529.9",
"protein_id": "ENSP00000345694.5",
"transcript_support_level": 5,
"aa_start": 3244,
"aa_end": null,
"aa_length": 3458,
"cds_start": 9730,
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.1487G>C",
"hgvs_p": null,
"transcript": "ENST00000679371.1",
"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": "ENST00000679371.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.9614G>C",
"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": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.3282G>C",
"hgvs_p": null,
"transcript": "ENST00000680248.1",
"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": "ENST00000680248.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.9730G>C",
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.2979G>C",
"hgvs_p": null,
"transcript": "ENST00000681364.1",
"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": "ENST00000681364.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"hgvs_c": "n.3954G>C",
"hgvs_p": null,
"transcript": "ENST00000681921.1",
"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": "ENST00000681921.1"
},
{
"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.308-22994C>G",
"hgvs_p": null,
"transcript": "ENST00000660729.1",
"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": "ENST00000660729.1"
},
{
"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.293-28579C>G",
"hgvs_p": null,
"transcript": "ENST00000841470.1",
"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": "ENST00000841470.1"
},
{
"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.305-403C>G",
"hgvs_p": null,
"transcript": "ENST00000841471.1",
"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": "ENST00000841471.1"
},
{
"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.1366-14629C>G",
"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": 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": "NR_110141.1"
}
],
"gene_symbol": "RELN",
"gene_hgnc_id": 9957,
"dbsnp": "rs73714410",
"frequency_reference_population": 0.000011152679,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000116296,
"gnomad_genomes_af": 0.00000657142,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9775981903076172,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.488,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5186,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.358,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 5,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BP6",
"BS1"
],
"verdict": "Likely_benign",
"transcript": "NM_005045.4",
"gene_symbol": "RELN",
"hgnc_id": 9957,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.9730G>C",
"hgvs_p": "p.Gly3244Arg"
},
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000422488.1",
"gene_symbol": "SLC26A5-AS1",
"hgnc_id": 55680,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1366-14629C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Familial temporal lobe epilepsy 7,Inborn genetic diseases,Norman-Roberts syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Norman-Roberts syndrome;Familial temporal lobe epilepsy 7|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}