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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: M-5553-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=5553&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 5553,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000000000",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNW",
"gene_hgnc_id": 7501,
"hgvs_c": "c.42T>C",
"hgvs_p": "p.Pro14Pro",
"transcript": "unassigned_transcript_4794",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 21,
"cds_start": 42,
"cds_end": null,
"cds_length": 68,
"cdna_start": 42,
"cdna_end": null,
"cdna_length": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TW",
"gene_hgnc_id": 7501,
"hgvs_c": "n.42T>C",
"hgvs_p": null,
"transcript": "ENST00000387382.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-ND2",
"gene_hgnc_id": 7456,
"hgvs_c": "c.*42T>C",
"hgvs_p": null,
"transcript": "ENST00000361453.3",
"protein_id": "ENSP00000355046.4",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 346,
"cds_start": -4,
"cds_end": null,
"cds_length": 1042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ND2",
"gene_hgnc_id": 7456,
"hgvs_c": "c.*42T>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_4793",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 346,
"cds_start": -4,
"cds_end": null,
"cds_length": 1042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNN",
"gene_hgnc_id": 7493,
"hgvs_c": "c.*104A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4796",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 23,
"cds_start": -4,
"cds_end": null,
"cds_length": 73,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 73,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNA",
"gene_hgnc_id": 7475,
"hgvs_c": "c.*34A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4795",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 22,
"cds_start": -4,
"cds_end": null,
"cds_length": 69,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 69,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNC",
"gene_hgnc_id": 7477,
"hgvs_c": "c.*208A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4797",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 21,
"cds_start": -4,
"cds_end": null,
"cds_length": 66,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 66,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TA",
"gene_hgnc_id": 7475,
"hgvs_c": "n.*34A>G",
"hgvs_p": null,
"transcript": "ENST00000387392.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 69,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TN",
"gene_hgnc_id": 7493,
"hgvs_c": "n.*104A>G",
"hgvs_p": null,
"transcript": "ENST00000387400.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 73,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TC",
"gene_hgnc_id": 7477,
"hgvs_c": "n.*208A>G",
"hgvs_p": null,
"transcript": "ENST00000387405.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 66,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRNW",
"gene_hgnc_id": 7501,
"dbsnp": "rs878853053",
"frequency_reference_population": 0.0015,
"hom_count_reference_population": 89,
"allele_count_reference_population": 89,
"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": 93,
"gnomad_mito_heteroplasmic": 7,
"computational_score_selected": 8.038439750671387,
"computational_prediction_selected": "Benign",
"computational_source_selected": "Mitotip",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.488,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": 8.038439750671387,
"mitotip_prediction": "Benign",
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP7,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP7",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRNW",
"hgnc_id": 7501,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.42T>C",
"hgvs_p": "p.Pro14Pro"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000387382.1",
"gene_symbol": "MT-TW",
"hgnc_id": 7501,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.42T>C",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000361453.3",
"gene_symbol": "MT-ND2",
"hgnc_id": 7456,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.*42T>C",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000000000",
"gene_symbol": "ND2",
"hgnc_id": 7456,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.*42T>C",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRNN",
"hgnc_id": 7493,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*104A>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRNA",
"hgnc_id": 7475,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*34A>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRNC",
"hgnc_id": 7477,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*208A>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000387392.1",
"gene_symbol": "MT-TA",
"hgnc_id": 7475,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*34A>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000387400.1",
"gene_symbol": "MT-TN",
"hgnc_id": 7493,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*104A>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000387405.1",
"gene_symbol": "MT-TC",
"hgnc_id": 7477,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*208A>G",
"hgvs_p": null
}
],
"clinvar_disease": "MELAS syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "not provided|MELAS syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}