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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: 5-142314648-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=142314648&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 142314648,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000434127.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg",
"transcript": "NM_001127496.3",
"protein_id": "NP_001120968.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 299,
"cds_start": 461,
"cds_end": null,
"cds_length": 900,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 4904,
"mane_select": "ENST00000434127.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg",
"transcript": "ENST00000434127.3",
"protein_id": "ENSP00000399468.2",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 299,
"cds_start": 461,
"cds_end": null,
"cds_length": 900,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 4904,
"mane_select": "NM_001127496.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.530A>G",
"hgvs_p": "p.Lys177Arg",
"transcript": "ENST00000344120.4",
"protein_id": "ENSP00000344967.4",
"transcript_support_level": 1,
"aa_start": 177,
"aa_end": null,
"aa_length": 322,
"cds_start": 530,
"cds_end": null,
"cds_length": 969,
"cdna_start": 717,
"cdna_end": null,
"cdna_length": 4938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.530A>G",
"hgvs_p": "p.Lys177Arg",
"transcript": "NM_030964.5",
"protein_id": "NP_112226.2",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 322,
"cds_start": 530,
"cds_end": null,
"cds_length": 969,
"cdna_start": 737,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg",
"transcript": "NM_001293289.3",
"protein_id": "NP_001280218.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 299,
"cds_start": 461,
"cds_end": null,
"cds_length": 900,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 5146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg",
"transcript": "NM_001293290.3",
"protein_id": "NP_001280219.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 299,
"cds_start": 461,
"cds_end": null,
"cds_length": 900,
"cdna_start": 866,
"cdna_end": null,
"cdna_length": 5084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.530A>G",
"hgvs_p": "p.Lys177Arg",
"transcript": "XM_011537685.4",
"protein_id": "XP_011535987.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 322,
"cds_start": 530,
"cds_end": null,
"cds_length": 969,
"cdna_start": 917,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg",
"transcript": "XM_017009910.3",
"protein_id": "XP_016865399.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 299,
"cds_start": 461,
"cds_end": null,
"cds_length": 900,
"cdna_start": 3174,
"cdna_end": null,
"cdna_length": 7392,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"hgvs_c": "n.1143A>G",
"hgvs_p": null,
"transcript": "ENST00000643792.1",
"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": 5349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPRY4",
"gene_hgnc_id": 15533,
"dbsnp": "rs78310959",
"frequency_reference_population": 0.0022679798,
"hom_count_reference_population": 6,
"allele_count_reference_population": 3661,
"gnomad_exomes_af": 0.00237435,
"gnomad_genomes_af": 0.00124723,
"gnomad_exomes_ac": 3471,
"gnomad_genomes_ac": 190,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.013789087533950806,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.205,
"revel_prediction": "Benign",
"alphamissense_score": 0.0979,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.645,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000434127.3",
"gene_symbol": "SPRY4",
"hgnc_id": 15533,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.461A>G",
"hgvs_p": "p.Lys154Arg"
}
],
"clinvar_disease": "Hypogonadotropic hypogonadism 17 with or without anosmia,SPRY4-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Hypogonadotropic hypogonadism 17 with or without anosmia|not provided|SPRY4-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}