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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-12018-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=12018&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 12018,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000361381.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-ND4",
"gene_hgnc_id": 7459,
"hgvs_c": "c.1259C>G",
"hgvs_p": "p.Thr420Ser",
"transcript": "ENST00000361381.2",
"protein_id": "ENSP00000354961.2",
"transcript_support_level": 6,
"aa_start": 420,
"aa_end": null,
"aa_length": 458,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1378,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ND4",
"gene_hgnc_id": 7459,
"hgvs_c": "c.1259C>G",
"hgvs_p": "p.Thr420Ser",
"transcript": "unassigned_transcript_4811",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 458,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1378,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNL2",
"gene_hgnc_id": 7491,
"hgvs_c": "c.-248C>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4814",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 22,
"cds_start": -4,
"cds_end": null,
"cds_length": 71,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 71,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNH",
"gene_hgnc_id": 7487,
"hgvs_c": "c.-120C>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4812",
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNS2",
"gene_hgnc_id": 7498,
"hgvs_c": "c.-189C>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4813",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 18,
"cds_start": -4,
"cds_end": null,
"cds_length": 59,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 59,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TH",
"gene_hgnc_id": 7487,
"hgvs_c": "n.-120C>G",
"hgvs_p": null,
"transcript": "ENST00000387441.1",
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TS2",
"gene_hgnc_id": 7498,
"hgvs_c": "n.-189C>G",
"hgvs_p": null,
"transcript": "ENST00000387449.1",
"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": 59,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TL2",
"gene_hgnc_id": 7491,
"hgvs_c": "n.-248C>G",
"hgvs_p": null,
"transcript": "ENST00000387456.1",
"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": 71,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MT-ND4",
"gene_hgnc_id": 7459,
"dbsnp": "rs1057516068",
"frequency_reference_population": 0,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"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": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.023789629340171814,
"computational_prediction_selected": "Benign",
"computational_source_selected": "Apogee2",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.1102,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.323,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": 0.023789629340171814,
"apogee2_prediction": "Benign",
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361381.2",
"gene_symbol": "MT-ND4",
"hgnc_id": 7459,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.1259C>G",
"hgvs_p": "p.Thr420Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "ND4",
"hgnc_id": 7459,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.1259C>G",
"hgvs_p": "p.Thr420Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNL2",
"hgnc_id": 7491,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-248C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNH",
"hgnc_id": 7487,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-120C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNS2",
"hgnc_id": 7498,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-189C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387441.1",
"gene_symbol": "MT-TH",
"hgnc_id": 7487,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-120C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387449.1",
"gene_symbol": "MT-TS2",
"hgnc_id": 7498,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-189C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387456.1",
"gene_symbol": "MT-TL2",
"hgnc_id": 7491,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-248C>G",
"hgvs_p": null
}
],
"clinvar_disease": "6 conditions,Congenital cardiomyopathy,Developmental delay,Hearing impairment,Leigh syndrome,Macrocephaly,Microcephaly",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Microcephaly;Developmental delay;Congenital cardiomyopathy;Hearing impairment|Macrocephaly;Developmental delay;Hearing impairment|6 conditions|Leigh syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}