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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: 10-26746333-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=26746333&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 26746333,
"ref": "A",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000376215.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.1108A>C",
"hgvs_p": "p.Ser370Arg",
"transcript": "NM_014317.5",
"protein_id": "NP_055132.2",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 415,
"cds_start": 1108,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1119,
"cdna_end": null,
"cdna_length": 1584,
"mane_select": "ENST00000376215.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.1108A>C",
"hgvs_p": "p.Ser370Arg",
"transcript": "ENST00000376215.10",
"protein_id": "ENSP00000365388.5",
"transcript_support_level": 1,
"aa_start": 370,
"aa_end": null,
"aa_length": 415,
"cds_start": 1108,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1119,
"cdna_end": null,
"cdna_length": 1584,
"mane_select": "NM_014317.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.917A>C",
"hgvs_p": "p.Glu306Ala",
"transcript": "NM_001321978.2",
"protein_id": "NP_001308907.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 306,
"cds_start": 917,
"cds_end": null,
"cds_length": 921,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 1393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.598A>C",
"hgvs_p": "p.Ser200Arg",
"transcript": "NM_001321979.2",
"protein_id": "NP_001308908.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 245,
"cds_start": 598,
"cds_end": null,
"cds_length": 738,
"cdna_start": 1202,
"cdna_end": null,
"cdna_length": 1667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.787A>C",
"hgvs_p": "p.Ser263Arg",
"transcript": "XM_017016011.3",
"protein_id": "XP_016871500.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 308,
"cds_start": 787,
"cds_end": null,
"cds_length": 927,
"cdna_start": 874,
"cdna_end": null,
"cdna_length": 1339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "c.739A>C",
"hgvs_p": "p.Ser247Arg",
"transcript": "XM_011519437.4",
"protein_id": "XP_011517739.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 292,
"cds_start": 739,
"cds_end": null,
"cds_length": 879,
"cdna_start": 901,
"cdna_end": null,
"cdna_length": 1366,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "n.350A>C",
"hgvs_p": null,
"transcript": "ENST00000470978.1",
"protein_id": null,
"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": 799,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "n.*213A>C",
"hgvs_p": null,
"transcript": "ENST00000491711.5",
"protein_id": "ENSP00000435695.1",
"transcript_support_level": 5,
"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": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"hgvs_c": "n.*213A>C",
"hgvs_p": null,
"transcript": "ENST00000491711.5",
"protein_id": "ENSP00000435695.1",
"transcript_support_level": 5,
"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": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDSS1",
"gene_hgnc_id": 17759,
"dbsnp": "rs1057519354",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8396618366241455,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.02199999988079071,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.596,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9876,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.096,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000715838005414123,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000376215.10",
"gene_symbol": "PDSS1",
"hgnc_id": 17759,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1108A>C",
"hgvs_p": "p.Ser370Arg"
}
],
"clinvar_disease": "Deafness-encephaloneuropathy-obesity-valvulopathy syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Deafness-encephaloneuropathy-obesity-valvulopathy syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}