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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: 9-35658680-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=35658680&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 35658680,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_174923.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "NM_174923.3",
"protein_id": "NP_777583.2",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 283,
"cds_start": 211,
"cds_end": null,
"cds_length": 852,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 1264,
"mane_select": "ENST00000426546.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000426546.7",
"protein_id": "ENSP00000414964.2",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 283,
"cds_start": 211,
"cds_end": null,
"cds_length": 852,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 1264,
"mane_select": "NM_174923.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000378409.7",
"protein_id": "ENSP00000367665.3",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 256,
"cds_start": 211,
"cds_end": null,
"cds_length": 771,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 1173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000327351.6",
"protein_id": "ENSP00000330327.2",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 155,
"cds_start": 211,
"cds_end": null,
"cds_length": 468,
"cdna_start": 274,
"cdna_end": null,
"cdna_length": 804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "NM_001195200.2",
"protein_id": "NP_001182129.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 256,
"cds_start": 211,
"cds_end": null,
"cds_length": 771,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 1183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "NM_001195201.2",
"protein_id": "NP_001182130.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 155,
"cds_start": 211,
"cds_end": null,
"cds_length": 468,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 1163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "NM_001195217.2",
"protein_id": "NP_001182146.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 139,
"cds_start": 211,
"cds_end": null,
"cds_length": 420,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 1236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000378407.7",
"protein_id": "ENSP00000367662.3",
"transcript_support_level": 2,
"aa_start": 71,
"aa_end": null,
"aa_length": 139,
"cds_start": 211,
"cds_end": null,
"cds_length": 420,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000378406.5",
"protein_id": "ENSP00000367661.1",
"transcript_support_level": 2,
"aa_start": 71,
"aa_end": null,
"aa_length": 137,
"cds_start": 211,
"cds_end": null,
"cds_length": 414,
"cdna_start": 277,
"cdna_end": null,
"cdna_length": 1016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "ENST00000421582.2",
"protein_id": "ENSP00000413003.2",
"transcript_support_level": 2,
"aa_start": 71,
"aa_end": null,
"aa_length": 119,
"cds_start": 211,
"cds_end": null,
"cds_length": 360,
"cdna_start": 274,
"cdna_end": null,
"cdna_length": 1324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val",
"transcript": "XM_005251403.6",
"protein_id": "XP_005251460.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 140,
"cds_start": 211,
"cds_end": null,
"cds_length": 423,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 915,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF39",
"gene_hgnc_id": 25909,
"hgvs_c": "n.*1642G>C",
"hgvs_p": null,
"transcript": "ENST00000490638.5",
"protein_id": "ENSP00000436756.1",
"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": 4498,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF39",
"gene_hgnc_id": 25909,
"hgvs_c": "n.*2475G>C",
"hgvs_p": null,
"transcript": "ENST00000475323.5",
"protein_id": "ENSP00000436519.1",
"transcript_support_level": 2,
"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": 2862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC107",
"gene_hgnc_id": 28465,
"dbsnp": "rs774349560",
"frequency_reference_population": 7.057332e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.05733e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3059963881969452,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.196,
"revel_prediction": "Benign",
"alphamissense_score": 0.1585,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.408,
"phylop100way_prediction": "Benign",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_174923.3",
"gene_symbol": "CCDC107",
"hgnc_id": 28465,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.211C>G",
"hgvs_p": "p.Leu71Val"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000490638.5",
"gene_symbol": "ARHGEF39",
"hgnc_id": 25909,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*1642G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}