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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: 8-107901086-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=107901086&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RSPO2",
"hgnc_id": 28583,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_178565.5",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000287949",
"hgnc_id": null,
"hgvs_c": "n.81-17084C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000665144.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.0651,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"chr": "8",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.053192704916000366,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 243,
"aa_ref": "A",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3084,
"cdna_start": 1314,
"cds_end": null,
"cds_length": 732,
"cds_start": 721,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_178565.5",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000276659.10",
"protein_coding": true,
"protein_id": "NP_848660.3",
"strand": false,
"transcript": "NM_178565.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 243,
"aa_ref": "A",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3084,
"cdna_start": 1314,
"cds_end": null,
"cds_length": 732,
"cds_start": 721,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000276659.10",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_178565.5",
"protein_coding": true,
"protein_id": "ENSP00000276659.5",
"strand": false,
"transcript": "ENST00000276659.10",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 179,
"aa_ref": "A",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2748,
"cdna_start": 978,
"cds_end": null,
"cds_length": 540,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000517781.5",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.529G>A",
"hgvs_p": "p.Ala177Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427937.1",
"strand": false,
"transcript": "ENST00000517781.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 176,
"aa_ref": "A",
"aa_start": 174,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2487,
"cdna_start": 717,
"cds_end": null,
"cds_length": 531,
"cds_start": 520,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000517939.5",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Ala174Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428940.1",
"strand": false,
"transcript": "ENST00000517939.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 243,
"aa_ref": "A",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2927,
"cdna_start": 1164,
"cds_end": null,
"cds_length": 732,
"cds_start": 721,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000971030.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641089.1",
"strand": false,
"transcript": "ENST00000971030.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 242,
"aa_ref": "A",
"aa_start": 240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3251,
"cdna_start": 1481,
"cds_end": null,
"cds_length": 729,
"cds_start": 718,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851102.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Ala240Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521161.1",
"strand": false,
"transcript": "ENST00000851102.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 239,
"aa_ref": "A",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2516,
"cdna_start": 1107,
"cds_end": null,
"cds_length": 720,
"cds_start": 709,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851104.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.709G>A",
"hgvs_p": "p.Ala237Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521163.1",
"strand": false,
"transcript": "ENST00000851104.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 180,
"aa_ref": "A",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2882,
"cdna_start": 1124,
"cds_end": null,
"cds_length": 543,
"cds_start": 532,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000971029.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Ala178Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641088.1",
"strand": false,
"transcript": "ENST00000971029.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 179,
"aa_ref": "A",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3165,
"cdna_start": 1395,
"cds_end": null,
"cds_length": 540,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001282863.2",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.529G>A",
"hgvs_p": "p.Ala177Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269792.1",
"strand": false,
"transcript": "NM_001282863.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 176,
"aa_ref": "A",
"aa_start": 174,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2487,
"cdna_start": 717,
"cds_end": null,
"cds_length": 531,
"cds_start": 520,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001317942.2",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Ala174Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304871.1",
"strand": false,
"transcript": "NM_001317942.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 69,
"aa_ref": "A",
"aa_start": 67,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2436,
"cdna_start": 669,
"cds_end": null,
"cds_length": 210,
"cds_start": 199,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000851103.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Ala67Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521162.1",
"strand": false,
"transcript": "ENST00000851103.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000666252.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "n.*800G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499279.1",
"strand": false,
"transcript": "ENST00000666252.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000666252.1",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "n.*800G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499279.1",
"strand": false,
"transcript": "ENST00000666252.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2932,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000665144.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000287949",
"hgvs_c": "n.81-17084C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000665144.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000521502.5",
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"hgvs_c": "n.*16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000521502.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs370736291",
"effect": "missense_variant",
"frequency_reference_population": 6.843194e-7,
"gene_hgnc_id": 28583,
"gene_symbol": "RSPO2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84319e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.345,
"pos": 107901086,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.177,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_178565.5"
}
]
}