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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: 2-44275766-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=44275766&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 44275766,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000260649.11",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "NM_000341.4",
"protein_id": "NP_000332.2",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 685,
"cds_start": 231,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 2969,
"mane_select": "ENST00000260649.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000260649.11",
"protein_id": "ENSP00000260649.6",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 685,
"cds_start": 231,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 2969,
"mane_select": "NM_000341.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000409229.7",
"protein_id": "ENSP00000386620.3",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 564,
"cds_start": 231,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 2909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000409387.5",
"protein_id": "ENSP00000387308.1",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 564,
"cds_start": 231,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 303,
"cdna_end": null,
"cdna_length": 2334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000409741.5",
"protein_id": "ENSP00000386954.1",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 502,
"cds_start": 231,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 1537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000410056.7",
"protein_id": "ENSP00000387337.3",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 391,
"cds_start": 231,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 1426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285542",
"gene_hgnc_id": null,
"hgvs_c": "n.*242T>A",
"hgvs_p": null,
"transcript": "ENST00000649044.1",
"protein_id": "ENSP00000497083.1",
"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": 3333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285542",
"gene_hgnc_id": null,
"hgvs_c": "n.*242T>A",
"hgvs_p": null,
"transcript": "ENST00000649044.1",
"protein_id": "ENSP00000497083.1",
"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": 3333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "ENST00000611973.4",
"protein_id": "ENSP00000483618.1",
"transcript_support_level": 5,
"aa_start": 77,
"aa_end": null,
"aa_length": 552,
"cds_start": 231,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 309,
"cdna_end": null,
"cdna_length": 1737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser",
"transcript": "XM_011533047.4",
"protein_id": "XP_011531349.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 564,
"cds_start": 231,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 5993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC3A1",
"gene_hgnc_id": 11025,
"dbsnp": "rs146630359",
"frequency_reference_population": 0.00327148,
"hom_count_reference_population": 12,
"allele_count_reference_population": 5281,
"gnomad_exomes_af": 0.00335456,
"gnomad_genomes_af": 0.00247437,
"gnomad_exomes_ac": 4904,
"gnomad_genomes_ac": 377,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8600000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.86,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.314,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS2_Supporting",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS2_Supporting"
],
"verdict": "Benign",
"transcript": "ENST00000260649.11",
"gene_symbol": "SLC3A1",
"hgnc_id": 11025,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.231T>A",
"hgvs_p": "p.Ser77Ser"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000649044.1",
"gene_symbol": "ENSG00000285542",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*242T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Cystinuria,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"phenotype_combined": "Cystinuria|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}