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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: 1-173857604-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=173857604&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 173857604,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000649689.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1837C>T",
"hgvs_p": "p.Leu613Phe",
"transcript": "NM_018122.5",
"protein_id": "NP_060592.2",
"transcript_support_level": null,
"aa_start": 613,
"aa_end": null,
"aa_length": 645,
"cds_start": 1837,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 2394,
"cdna_end": null,
"cdna_length": 3336,
"mane_select": "ENST00000649689.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1837C>T",
"hgvs_p": "p.Leu613Phe",
"transcript": "ENST00000649689.2",
"protein_id": "ENSP00000497569.1",
"transcript_support_level": null,
"aa_start": 613,
"aa_end": null,
"aa_length": 645,
"cds_start": 1837,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 2394,
"cdna_end": null,
"cdna_length": 3336,
"mane_select": "NM_018122.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1774C>T",
"hgvs_p": "p.Leu592Phe",
"transcript": "ENST00000647645.1",
"protein_id": "ENSP00000497450.1",
"transcript_support_level": null,
"aa_start": 592,
"aa_end": null,
"aa_length": 624,
"cds_start": 1774,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 2296,
"cdna_end": null,
"cdna_length": 3209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1684C>T",
"hgvs_p": "p.Leu562Phe",
"transcript": "NM_001365212.1",
"protein_id": "NP_001352141.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 594,
"cds_start": 1684,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 2241,
"cdna_end": null,
"cdna_length": 3183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1684C>T",
"hgvs_p": "p.Leu562Phe",
"transcript": "ENST00000648807.1",
"protein_id": "ENSP00000497472.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 594,
"cds_start": 1684,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 2261,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.1354C>T",
"hgvs_p": "p.Leu452Phe",
"transcript": "ENST00000648960.1",
"protein_id": "ENSP00000497091.1",
"transcript_support_level": null,
"aa_start": 452,
"aa_end": null,
"aa_length": 484,
"cds_start": 1354,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1931,
"cdna_end": null,
"cdna_length": 2716,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*1416C>T",
"hgvs_p": null,
"transcript": "ENST00000471476.2",
"protein_id": "ENSP00000497663.1",
"transcript_support_level": 4,
"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": 3075,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*1527C>T",
"hgvs_p": null,
"transcript": "ENST00000647730.1",
"protein_id": "ENSP00000497781.1",
"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": 3133,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*981C>T",
"hgvs_p": null,
"transcript": "ENST00000647788.1",
"protein_id": "ENSP00000497769.1",
"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": 2997,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*2303C>T",
"hgvs_p": null,
"transcript": "ENST00000648271.1",
"protein_id": "ENSP00000497795.1",
"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": 3361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "c.*840C>T",
"hgvs_p": null,
"transcript": "ENST00000649067.1",
"protein_id": "ENSP00000497052.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3820,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*1416C>T",
"hgvs_p": null,
"transcript": "ENST00000471476.2",
"protein_id": "ENSP00000497663.1",
"transcript_support_level": 4,
"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": 3075,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*1527C>T",
"hgvs_p": null,
"transcript": "ENST00000647730.1",
"protein_id": "ENSP00000497781.1",
"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": 3133,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*981C>T",
"hgvs_p": null,
"transcript": "ENST00000647788.1",
"protein_id": "ENSP00000497769.1",
"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": 2997,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"hgvs_c": "n.*2303C>T",
"hgvs_p": null,
"transcript": "ENST00000648271.1",
"protein_id": "ENSP00000497795.1",
"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": 3361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "GAS5",
"gene_hgnc_id": 16355,
"hgvs_c": "n.518+1604G>A",
"hgvs_p": null,
"transcript": "ENST00000827943.1",
"protein_id": null,
"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": 697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DARS2",
"gene_hgnc_id": 25538,
"dbsnp": "rs121918212",
"frequency_reference_population": 0.0000024782503,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205217,
"gnomad_genomes_af": 0.00000657151,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9086124897003174,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.849,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1976,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.06,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000649689.2",
"gene_symbol": "DARS2",
"hgnc_id": 25538,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1837C>T",
"hgvs_p": "p.Leu613Phe"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000827943.1",
"gene_symbol": "GAS5",
"hgnc_id": 16355,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.518+1604G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}