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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: 6-73783709-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=73783709&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 73783709,
"ref": "A",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000287097.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.2108A>C",
"hgvs_p": "p.Tyr703Ser",
"transcript": "NM_133493.5",
"protein_id": "NP_598000.2",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 1445,
"cds_start": 2108,
"cds_end": null,
"cds_length": 4338,
"cdna_start": 2121,
"cdna_end": null,
"cdna_length": 9031,
"mane_select": "ENST00000287097.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.2108A>C",
"hgvs_p": "p.Tyr703Ser",
"transcript": "ENST00000287097.6",
"protein_id": "ENSP00000287097.4",
"transcript_support_level": 1,
"aa_start": 703,
"aa_end": null,
"aa_length": 1445,
"cds_start": 2108,
"cds_end": null,
"cds_length": 4338,
"cdna_start": 2121,
"cdna_end": null,
"cdna_length": 9031,
"mane_select": "NM_133493.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.2108A>C",
"hgvs_p": "p.Tyr703Ser",
"transcript": "ENST00000437994.6",
"protein_id": "ENSP00000388062.2",
"transcript_support_level": 1,
"aa_start": 703,
"aa_end": null,
"aa_length": 1428,
"cds_start": 2108,
"cds_end": null,
"cds_length": 4287,
"cdna_start": 2539,
"cdna_end": null,
"cdna_length": 9401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1877A>C",
"hgvs_p": "p.Tyr626Ser",
"transcript": "ENST00000422508.6",
"protein_id": "ENSP00000404475.2",
"transcript_support_level": 1,
"aa_start": 626,
"aa_end": null,
"aa_length": 1368,
"cds_start": 1877,
"cds_end": null,
"cds_length": 4107,
"cdna_start": 2308,
"cdna_end": null,
"cdna_length": 9221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.2108A>C",
"hgvs_p": "p.Tyr703Ser",
"transcript": "NM_001159587.3",
"protein_id": "NP_001153059.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 1428,
"cds_start": 2108,
"cds_end": null,
"cds_length": 4287,
"cdna_start": 2121,
"cdna_end": null,
"cdna_length": 8980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1877A>C",
"hgvs_p": "p.Tyr626Ser",
"transcript": "NM_001159588.3",
"protein_id": "NP_001153060.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 1368,
"cds_start": 1877,
"cds_end": null,
"cds_length": 4107,
"cdna_start": 1890,
"cdna_end": null,
"cdna_length": 8800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.2069A>C",
"hgvs_p": "p.Tyr690Ser",
"transcript": "XM_047418211.1",
"protein_id": "XP_047274167.1",
"transcript_support_level": null,
"aa_start": 690,
"aa_end": null,
"aa_length": 1432,
"cds_start": 2069,
"cds_end": null,
"cds_length": 4299,
"cdna_start": 2084,
"cdna_end": null,
"cdna_length": 8994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1388A>C",
"hgvs_p": "p.Tyr463Ser",
"transcript": "XM_047418212.1",
"protein_id": "XP_047274168.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1388,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 1880,
"cdna_end": null,
"cdna_length": 8790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1388A>C",
"hgvs_p": "p.Tyr463Ser",
"transcript": "XM_047418213.1",
"protein_id": "XP_047274169.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1388,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 2092,
"cdna_end": null,
"cdna_length": 9002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1388A>C",
"hgvs_p": "p.Tyr463Ser",
"transcript": "XM_047418214.1",
"protein_id": "XP_047274170.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1388,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 2125,
"cdna_end": null,
"cdna_length": 9035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1388A>C",
"hgvs_p": "p.Tyr463Ser",
"transcript": "XM_047418215.1",
"protein_id": "XP_047274171.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1388,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 1998,
"cdna_end": null,
"cdna_length": 8908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.1388A>C",
"hgvs_p": "p.Tyr463Ser",
"transcript": "XM_047418216.1",
"protein_id": "XP_047274172.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1388,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 2182,
"cdna_end": null,
"cdna_length": 9092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "c.389A>C",
"hgvs_p": "p.Tyr130Ser",
"transcript": "XM_047418217.1",
"protein_id": "XP_047274173.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 872,
"cds_start": 389,
"cds_end": null,
"cds_length": 2619,
"cdna_start": 451,
"cdna_end": null,
"cdna_length": 7361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"hgvs_c": "n.2080A>C",
"hgvs_p": null,
"transcript": "ENST00000649530.1",
"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": 3516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CD109",
"gene_hgnc_id": 21685,
"dbsnp": "rs10455097",
"frequency_reference_population": 0.5135052,
"hom_count_reference_population": 209847,
"allele_count_reference_population": 807831,
"gnomad_exomes_af": 0.51056,
"gnomad_genomes_af": 0.541049,
"gnomad_exomes_ac": 725611,
"gnomad_genomes_ac": 82220,
"gnomad_exomes_homalt": 187106,
"gnomad_genomes_homalt": 22741,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000040415843614027835,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.034,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.166,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000287097.6",
"gene_symbol": "CD109",
"hgnc_id": 21685,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2108A>C",
"hgvs_p": "p.Tyr703Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}