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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: 2-196848023-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196848023&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 196848023,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000354764.9",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1876T>C",
"hgvs_p": "p.Tyr626His",
"transcript": "NM_024989.4",
"protein_id": "NP_079265.2",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 922,
"cds_start": 1876,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 1967,
"cdna_end": null,
"cdna_length": 11090,
"mane_select": "ENST00000354764.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1876T>C",
"hgvs_p": "p.Tyr626His",
"transcript": "ENST00000354764.9",
"protein_id": "ENSP00000346809.3",
"transcript_support_level": 1,
"aa_start": 626,
"aa_end": null,
"aa_length": 922,
"cds_start": 1876,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 1967,
"cdna_end": null,
"cdna_length": 11090,
"mane_select": "NM_024989.4",
"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": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*1807T>C",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"transcript_support_level": 1,
"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": 8942,
"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": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*1807T>C",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"transcript_support_level": 1,
"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": 8942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1354T>C",
"hgvs_p": "p.Tyr452His",
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": 452,
"aa_end": null,
"aa_length": 748,
"cds_start": 1354,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 2051,
"cdna_end": null,
"cdna_length": 11174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.709T>C",
"hgvs_p": "p.Tyr237His",
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 533,
"cds_start": 709,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1911,
"cdna_end": null,
"cdna_length": 11034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1354T>C",
"hgvs_p": "p.Tyr452His",
"transcript": "XM_017004992.1",
"protein_id": "XP_016860481.1",
"transcript_support_level": null,
"aa_start": 452,
"aa_end": null,
"aa_length": 748,
"cds_start": 1354,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1822,
"cdna_end": null,
"cdna_length": 10945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1354T>C",
"hgvs_p": "p.Tyr452His",
"transcript": "XM_017004993.2",
"protein_id": "XP_016860482.1",
"transcript_support_level": null,
"aa_start": 452,
"aa_end": null,
"aa_length": 748,
"cds_start": 1354,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 2391,
"cdna_end": null,
"cdna_length": 11514,
"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": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.1340T>C",
"hgvs_p": null,
"transcript": "ENST00000470179.5",
"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": 2874,
"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": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.1873T>C",
"hgvs_p": null,
"transcript": "XR_007082522.1",
"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": 2049,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.*3T>C",
"hgvs_p": null,
"transcript": "ENST00000409475.5",
"protein_id": "ENSP00000387028.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 592,
"cds_start": -4,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"dbsnp": "rs150893861",
"frequency_reference_population": 0.000504072,
"hom_count_reference_population": 0,
"allele_count_reference_population": 806,
"gnomad_exomes_af": 0.000490039,
"gnomad_genomes_af": 0.000637512,
"gnomad_exomes_ac": 709,
"gnomad_genomes_ac": 97,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007993310689926147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.199,
"revel_prediction": "Benign",
"alphamissense_score": 0.3302,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.039,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000354764.9",
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1876T>C",
"hgvs_p": "p.Tyr626His"
}
],
"clinvar_disease": " autosomal recessive 42,Hereditary spastic paraplegia,Intellectual disability",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Intellectual disability, autosomal recessive 42|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}