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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: 1-37612843-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=37612843&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 37612843,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001038633.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "NM_001242908.2",
"protein_id": "NP_001229837.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000356545.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001242908.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000356545.7",
"protein_id": "ENSP00000348944.2",
"transcript_support_level": 1,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001242908.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356545.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000401068.1",
"protein_id": "ENSP00000383846.1",
"transcript_support_level": 1,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000401068.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ala172Val",
"transcript": "ENST00000612451.4",
"protein_id": "ENSP00000479832.1",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 200,
"cds_start": 515,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000612451.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.740C>T",
"hgvs_p": "p.Ala247Val",
"transcript": "ENST00000866283.1",
"protein_id": "ENSP00000536342.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 275,
"cds_start": 740,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866283.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "NM_001038633.4",
"protein_id": "NP_001033722.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001038633.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000866279.1",
"protein_id": "ENSP00000536338.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866279.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000866280.1",
"protein_id": "ENSP00000536339.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866280.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000866281.1",
"protein_id": "ENSP00000536340.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866281.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000866282.1",
"protein_id": "ENSP00000536341.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866282.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.623C>T",
"hgvs_p": "p.Ala208Val",
"transcript": "NM_001242909.2",
"protein_id": "NP_001229838.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 236,
"cds_start": 623,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001242909.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.623C>T",
"hgvs_p": "p.Ala208Val",
"transcript": "ENST00000615459.4",
"protein_id": "ENSP00000481178.1",
"transcript_support_level": 2,
"aa_start": 208,
"aa_end": null,
"aa_length": 236,
"cds_start": 623,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000615459.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Ala184Val",
"transcript": "ENST00000967724.1",
"protein_id": "ENSP00000637783.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 212,
"cds_start": 551,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967724.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ala172Val",
"transcript": "NM_001242910.2",
"protein_id": "NP_001229839.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 200,
"cds_start": 515,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001242910.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.365C>T",
"hgvs_p": "p.Ala122Val",
"transcript": "ENST00000866284.1",
"protein_id": "ENSP00000536343.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 150,
"cds_start": 365,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866284.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "XM_006710583.5",
"protein_id": "XP_006710646.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 263,
"cds_start": 704,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710583.5"
}
],
"gene_symbol": "RSPO1",
"gene_hgnc_id": 21679,
"dbsnp": "rs201963347",
"frequency_reference_population": 0.00002230638,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000205253,
"gnomad_genomes_af": 0.0000394016,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05769798159599304,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.143,
"revel_prediction": "Benign",
"alphamissense_score": 0.0855,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.743,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001038633.4",
"gene_symbol": "RSPO1",
"hgnc_id": 21679,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}