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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: 4-107644918-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=107644918&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 107644918,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005443.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1390C>G",
"hgvs_p": "p.Pro464Ala",
"transcript": "NM_005443.5",
"protein_id": "NP_005434.4",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 624,
"cds_start": 1390,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265174.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005443.5"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1390C>G",
"hgvs_p": "p.Pro464Ala",
"transcript": "ENST00000265174.5",
"protein_id": "ENSP00000265174.4",
"transcript_support_level": 1,
"aa_start": 464,
"aa_end": null,
"aa_length": 624,
"cds_start": 1390,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005443.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265174.5"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1459C>G",
"hgvs_p": "p.Pro487Ala",
"transcript": "ENST00000873396.1",
"protein_id": "ENSP00000543455.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 647,
"cds_start": 1459,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873396.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1387C>G",
"hgvs_p": "p.Pro463Ala",
"transcript": "ENST00000970503.1",
"protein_id": "ENSP00000640562.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 623,
"cds_start": 1387,
"cds_end": null,
"cds_length": 1872,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970503.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1390C>G",
"hgvs_p": "p.Pro464Ala",
"transcript": "ENST00000931561.1",
"protein_id": "ENSP00000601620.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 622,
"cds_start": 1390,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931561.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1381C>G",
"hgvs_p": "p.Pro461Ala",
"transcript": "ENST00000931560.1",
"protein_id": "ENSP00000601619.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 621,
"cds_start": 1381,
"cds_end": null,
"cds_length": 1866,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931560.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1378C>G",
"hgvs_p": "p.Pro460Ala",
"transcript": "ENST00000970505.1",
"protein_id": "ENSP00000640564.1",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 620,
"cds_start": 1378,
"cds_end": null,
"cds_length": 1863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970505.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1336C>G",
"hgvs_p": "p.Pro446Ala",
"transcript": "ENST00000970504.1",
"protein_id": "ENSP00000640563.1",
"transcript_support_level": null,
"aa_start": 446,
"aa_end": null,
"aa_length": 606,
"cds_start": 1336,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970504.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.937C>G",
"hgvs_p": "p.Pro313Ala",
"transcript": "ENST00000931559.1",
"protein_id": "ENSP00000601618.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 473,
"cds_start": 937,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931559.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.757C>G",
"hgvs_p": "p.Pro253Ala",
"transcript": "ENST00000931563.1",
"protein_id": "ENSP00000601622.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 413,
"cds_start": 757,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931563.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1327C>G",
"hgvs_p": "p.Pro443Ala",
"transcript": "XM_011532400.3",
"protein_id": "XP_011530702.1",
"transcript_support_level": null,
"aa_start": 443,
"aa_end": null,
"aa_length": 603,
"cds_start": 1327,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532400.3"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1327C>G",
"hgvs_p": "p.Pro443Ala",
"transcript": "XM_011532401.2",
"protein_id": "XP_011530703.1",
"transcript_support_level": null,
"aa_start": 443,
"aa_end": null,
"aa_length": 603,
"cds_start": 1327,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532401.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.670-13058C>G",
"hgvs_p": null,
"transcript": "ENST00000931562.1",
"protein_id": "ENSP00000601621.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 345,
"cds_start": null,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931562.1"
}
],
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"dbsnp": "rs544807411",
"frequency_reference_population": 0.0000027364124,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273641,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8814228773117065,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.624,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8691,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.382,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005443.5",
"gene_symbol": "PAPSS1",
"hgnc_id": 8603,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1390C>G",
"hgvs_p": "p.Pro464Ala"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}