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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: 15-42731275-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42731275&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 42731275,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000356231.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.Asn599Ser",
"transcript": "NM_138477.4",
"protein_id": "NP_612486.2",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 1227,
"cds_start": 1796,
"cds_end": null,
"cds_length": 3684,
"cdna_start": 1822,
"cdna_end": null,
"cdna_length": 4657,
"mane_select": "ENST00000356231.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.Asn599Ser",
"transcript": "ENST00000356231.4",
"protein_id": "ENSP00000348564.3",
"transcript_support_level": 1,
"aa_start": 599,
"aa_end": null,
"aa_length": 1227,
"cds_start": 1796,
"cds_end": null,
"cds_length": 3684,
"cdna_start": 1822,
"cdna_end": null,
"cdna_length": 4657,
"mane_select": "NM_138477.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1823A>G",
"hgvs_p": "p.Asn608Ser",
"transcript": "XM_011521270.3",
"protein_id": "XP_011519572.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 1236,
"cds_start": 1823,
"cds_end": null,
"cds_length": 3711,
"cdna_start": 1849,
"cdna_end": null,
"cdna_length": 4684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1820A>G",
"hgvs_p": "p.Asn607Ser",
"transcript": "XM_011521271.3",
"protein_id": "XP_011519573.1",
"transcript_support_level": null,
"aa_start": 607,
"aa_end": null,
"aa_length": 1235,
"cds_start": 1820,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 1846,
"cdna_end": null,
"cdna_length": 4681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1799A>G",
"hgvs_p": "p.Asn600Ser",
"transcript": "XM_005254176.6",
"protein_id": "XP_005254233.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 1228,
"cds_start": 1799,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 1825,
"cdna_end": null,
"cdna_length": 4660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1823A>G",
"hgvs_p": "p.Asn608Ser",
"transcript": "XM_047432193.1",
"protein_id": "XP_047288149.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 1084,
"cds_start": 1823,
"cds_end": null,
"cds_length": 3255,
"cdna_start": 1849,
"cdna_end": null,
"cdna_length": 3439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.1823A>G",
"hgvs_p": "p.Asn608Ser",
"transcript": "XM_047432194.1",
"protein_id": "XP_047288150.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 1025,
"cds_start": 1823,
"cds_end": null,
"cds_length": 3078,
"cdna_start": 1849,
"cdna_end": null,
"cdna_length": 3192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.788A>G",
"hgvs_p": "p.Asn263Ser",
"transcript": "XM_011521274.3",
"protein_id": "XP_011519576.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 891,
"cds_start": 788,
"cds_end": null,
"cds_length": 2676,
"cdna_start": 899,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "c.788A>G",
"hgvs_p": "p.Asn263Ser",
"transcript": "XM_047432195.1",
"protein_id": "XP_047288151.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 891,
"cds_start": 788,
"cds_end": null,
"cds_length": 2676,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 3889,
"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": 10,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "n.*974A>G",
"hgvs_p": null,
"transcript": "ENST00000643434.1",
"protein_id": "ENSP00000494699.1",
"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": 3901,
"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": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "n.1849A>G",
"hgvs_p": null,
"transcript": "XR_931757.3",
"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": 2277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"hgvs_c": "n.*974A>G",
"hgvs_p": null,
"transcript": "ENST00000643434.1",
"protein_id": "ENSP00000494699.1",
"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": 3901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDAN1",
"gene_hgnc_id": 1713,
"dbsnp": "rs120074166",
"frequency_reference_population": 0.000021684637,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000225739,
"gnomad_genomes_af": 0.0000131425,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8864743709564209,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.613,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1379,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.479,
"phylop100way_prediction": "Uncertain_significance",
"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": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000356231.4",
"gene_symbol": "CDAN1",
"hgnc_id": 1713,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.Asn599Ser"
}
],
"clinvar_disease": " congenital dyserythropoietic, type 1a, type I,Anemia,Congenital dyserythropoietic anemia",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "Congenital dyserythropoietic anemia, type I|Anemia, congenital dyserythropoietic, type 1a",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}