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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: 5-7901117-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=7901117&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 7901117,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,non_coding_transcript_exon_variant",
"transcript": "ENST00000506115.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "ENST00000264668.6",
"protein_id": "ENSP00000264668.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 725,
"cds_start": -4,
"cds_end": null,
"cds_length": 2178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "n.618T>C",
"hgvs_p": null,
"transcript": "ENST00000506115.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 620,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "n.51T>C",
"hgvs_p": null,
"transcript": "ENST00000509379.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 455,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "n.*2825T>C",
"hgvs_p": null,
"transcript": "ENST00000511461.5",
"protein_id": "ENSP00000424719.1",
"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": 3076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "n.*2825T>C",
"hgvs_p": null,
"transcript": "ENST00000511461.5",
"protein_id": "ENSP00000424719.1",
"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": 3076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "NM_002454.3",
"protein_id": "NP_002445.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3245,
"mane_select": "ENST00000440940.7",
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "ENST00000440940.7",
"protein_id": "ENSP00000402510.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3245,
"mane_select": "NM_002454.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "NM_001364440.2",
"protein_id": "NP_001351369.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "NM_001364441.2",
"protein_id": "NP_001351370.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "NM_001364442.2",
"protein_id": "NP_001351371.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRR",
"gene_hgnc_id": 7473,
"hgvs_c": "c.*1059T>C",
"hgvs_p": null,
"transcript": "NM_024010.4",
"protein_id": "NP_076915.3",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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},
{
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"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 13,
"intron_rank": null,
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"gene_symbol": "MTRR",
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"hgvs_c": "n.*1975T>C",
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"transcript": "ENST00000510525.5",
"protein_id": "ENSP00000421991.1",
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"aa_start": null,
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"aa_length": null,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 15,
"intron_rank": null,
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"gene_symbol": "MTRR",
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"hgvs_c": "n.*4T>C",
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"transcript": "NR_134480.2",
"protein_id": null,
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},
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"strand": true,
"consequences": [
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],
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"exon_count": 14,
"intron_rank": null,
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"gene_symbol": "MTRR",
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"hgvs_c": "n.*4T>C",
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},
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],
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 15,
"intron_rank": null,
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"gene_symbol": "MTRR",
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},
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],
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},
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],
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},
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],
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"intron_rank": null,
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],
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],
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},
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],
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"feature": null
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
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"exon_count": 16,
"intron_rank": null,
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"transcript": "NR_157175.2",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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}
],
"gene_symbol": "MTRR",
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"dbsnp": "rs10520873",
"frequency_reference_population": 0.21893242,
"hom_count_reference_population": 4397,
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"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.218932,
"gnomad_exomes_ac": 0,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": -0.8899999856948853,
"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": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.144,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
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"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": "ENST00000506115.1",
"gene_symbol": "MTRR",
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"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
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}
],
"clinvar_disease": "Disorders of Intracellular Cobalamin Metabolism,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Disorders of Intracellular Cobalamin Metabolism|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}