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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: 6-31874821-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31874821&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31874821,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000229729.11",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Asp123Val",
"transcript": "NM_025257.3",
"protein_id": "NP_079533.2",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 710,
"cds_start": 368,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 385,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": "ENST00000229729.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Asp123Val",
"transcript": "ENST00000229729.11",
"protein_id": "ENSP00000229729.6",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 710,
"cds_start": 368,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 385,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": "NM_025257.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.353A>T",
"hgvs_p": "p.Asp118Val",
"transcript": "ENST00000414427.1",
"protein_id": "ENSP00000398901.1",
"transcript_support_level": 5,
"aa_start": 118,
"aa_end": null,
"aa_length": 409,
"cds_start": 353,
"cds_end": null,
"cds_length": 1231,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 1233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.140A>T",
"hgvs_p": "p.Asp47Val",
"transcript": "NM_001178045.2",
"protein_id": "NP_001171516.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 634,
"cds_start": 140,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 2637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.140A>T",
"hgvs_p": "p.Asp47Val",
"transcript": "ENST00000544672.5",
"protein_id": "ENSP00000444109.1",
"transcript_support_level": 2,
"aa_start": 47,
"aa_end": null,
"aa_length": 634,
"cds_start": 140,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 2634,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "n.385A>T",
"hgvs_p": null,
"transcript": "ENST00000465707.5",
"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": 681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 20,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.342+108A>T",
"hgvs_p": null,
"transcript": "NM_001178044.2",
"protein_id": "NP_001171515.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": -4,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 20,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "c.342+108A>T",
"hgvs_p": null,
"transcript": "ENST00000375562.8",
"protein_id": "ENSP00000364712.4",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": -4,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"hgvs_c": "n.*1A>T",
"hgvs_p": null,
"transcript": "ENST00000462671.1",
"protein_id": null,
"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": 426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC44A4",
"gene_hgnc_id": 13941,
"dbsnp": "rs12661281",
"frequency_reference_population": 0.1337312,
"hom_count_reference_population": 16109,
"allele_count_reference_population": 215633,
"gnomad_exomes_af": 0.135767,
"gnomad_genomes_af": 0.114113,
"gnomad_exomes_ac": 198331,
"gnomad_genomes_ac": 17302,
"gnomad_exomes_homalt": 14785,
"gnomad_genomes_homalt": 1324,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0044405460357666016,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.045,
"revel_prediction": "Benign",
"alphamissense_score": 0.0661,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.874,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000229729.11",
"gene_symbol": "SLC44A4",
"hgnc_id": 13941,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Asp123Val"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}